From 6816190306440b9559c5f1aa637eedf43dab0b2a Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Mon, 30 Jun 2025 13:31:31 -0400
Subject: [PATCH 01/53] pixi configurations added

---
 pyproject.toml | 100 +++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 97 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1f012b30..bee5be63 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,14 +4,14 @@ description = "Spectroscopy Histogram Visualizer for Event Reduction"
 dynamic = ["version"]
 requires-python = ">=3.10"
 dependencies = [
-    "mantidworkbench >= 6.12",
-    "pyoncat ~= 1.6",
-    "configupdater"
 ]
+readme = "README.md"
 license = { text = "GPL3.0" }
 
 [project.urls]
 homepage = "https://github.com/neutrons/Shiver/"
+repository = "https://github.com/neutrons/Shiver/"
+documentation = "https://neutrons.github.io/Shiver/"
 
 [build-system]
 requires = [
@@ -56,3 +56,97 @@ disable = ["too-many-locals",
            "duplicate-code"
 ]
 extension-pkg-whitelist = ["PyQt5"]
+
+# ------------------ #
+# Pixi configuration #
+# ------------------ #
+[tool.pixi.workspace]
+preview = ["pixi-build"] # Need this to access pixi-build feature
+platforms = ["linux-64"]
+channels = [
+  "conda-forge",
+  "https://prefix.dev/pixi-build-backends",
+  "mantid-ornl",
+  "mantid",
+  "neutrons",
+  "neutrons/label/rc",
+  "oncat"
+]
+
+
+[tool.pixi.package]
+name = "shiver"
+version = "0.0.0" # placeholder, can be updated by task sync-version
+
+[tool.pixi.package.build]
+backend = { name = "pixi-build-python", version = "0.1.*" }
+
+[tool.pixi.package.host-dependencies]
+hatchling = "*"
+versioningit = "*"
+
+[tool.pixi.package.run-dependencies]
+toml = "*"
+
+[tool.pixi.dependencies]
+toml = ">=0.10.2,<0.11"
+mantidworkbench = ">=6.12"
+pyoncat = ">=2.1"
+pyoncatqt =">=1.2.0"
+configupdater = "*"
+
+[tool.pixi.pypi-dependencies]
+shiver = { path = ".", editable = true }
+toml-cli = ">=0.7.0,<0.8"
+pyoncat = "*"
+configupdater = "*"
+
+[tool.pixi.environments]
+default = { features = ["package", "developer"], solve-group = "default" }
+
+[tool.pixi.feature.package.dependencies]
+anaconda-client = ">=1.13.0,<2"
+twine = ">=6.1.0,<7"
+versioningit = "*"
+hatch = "*"
+
+[tool.pixi.feature.developer.dependencies]
+pip = "*"
+versioningit = "*"
+pre-commit = "*"
+pip-audit = ">=2.9.0,<3"
+pylint = "*"
+sphinx = ">=8"
+sphinx_rtd_theme = ">=3.0.1"
+codecov = ">=2.1.13"
+pytest = ">=8.4.1"
+pytest-qt = ">=4.4.0"
+pytest-cov = ">=6.2.1"
+pytest-mock = ">=3.14.1"
+pytest-xvfb = ">=3.1.1"
+
+[tool.pixi.tasks]
+# PyPI
+build-sdist = { cmd = "hatch build sdist", description = "Build the source distribution (tar.gz)" }
+build-pypi = { cmd = "hatch build", description = "Build the package for PyPI" }
+clean-pypi = { cmd = "rm -rf dist", description = "Clean the PyPI build artifacts" }
+publish-pypi = { cmd = "twine upload dist/*", description = "Publish the package to PyPI", depends-on = [
+  "build-pypi",
+] }
+# Conda
+build-conda-command = { cmd = "pixi build", description = "Build the conda package command" }
+build-conda = { description = "Build the conda package", depends-on = [
+  "sync-version",
+  "build-conda-command",
+  "reset-version",
+] }
+clean-conda = { cmd = "rm shiver-*.conda", description = "Clean the conda build artifacts" }
+# MISC
+clean-all = { description = "Clean all build artifacts", depends-on = [
+  "reset-version",
+  "clean-pypi",
+  "clean-conda",
+] }
+sync-version = { cmd = "version=$(python -m versioningit); toml set tool.pixi.package.version \"$version\" --toml-path pyproject.toml" }
+reset-version = { cmd = "toml set tool.pixi.package.version \"0.0.0\" --toml-path pyproject.toml", description = "Reset the package version to 0.0.0" }
+audit-deps = { cmd = "pip-audit --local -s osv" }

From beaeee14705725cda18b30c535b2fb484664ffff Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Mon, 30 Jun 2025 16:29:49 -0400
Subject: [PATCH 02/53] pixi environments configurations, environment and meta
 files remoced, gitingore update

---
 .gitignore             |  2 ++
 conda.recipe/meta.yaml | 49 ------------------------------------------
 environment.yml        | 32 ---------------------------
 pyproject.toml         | 20 +++++++++++------
 4 files changed, 15 insertions(+), 88 deletions(-)
 delete mode 100644 conda.recipe/meta.yaml
 delete mode 100644 environment.yml

diff --git a/.gitignore b/.gitignore
index 6028f484..4a560c5b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -130,3 +130,5 @@ dmypy.json
 
 src/shiver/_version.py
 .vscode/launch.json
+# pixi environments
+.pixi
diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
deleted file mode 100644
index 615a4862..00000000
--- a/conda.recipe/meta.yaml
+++ /dev/null
@@ -1,49 +0,0 @@
-# load information from pyproject.toml
-{% set pyproject = load_file_data('pyproject.toml') %}
-{% set project = pyproject.get('project', {}) %}
-{% set license = project.get('license').get('text') %}
-{% set description = project.get('description') %}
-{% set project_url = pyproject.get('project', {}).get('urls') %}
-{% set url = project_url.get('homepage') %}
-# this will get the version set by environment variable
-{% set version = environ.get('VERSION') %}
-{% set git_describe_number = environ.get('GIT_DESCRIBE_NUMBER', '0') | string %}
-
-package:
-  name: shiver
-  version: {{ version }}
-
-source:
-  path: ..
-
-build:
-  noarch: python
-  number: {{ git_describe_number }}
-  string: py{{py}}
-  script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv
-
-requirements:
-  host:
-    - python
-    - versioningit
-
-  build:
-    - setuptools
-    - versioningit
-
-  run:
-    - mantidworkbench
-    - pyoncat
-    - pyoncatqt
-    - configupdater
-
-  test:
-    imports:
-      - shiver
-
-about:
-  home: {{ url }}
-  license: {{ license }}
-  license_family: GPL
-  license_file: ../LICENSE
-  summary: {{ description }}
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index 3a5c2028..00000000
--- a/environment.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-name: shiver
-channels:
-  - conda-forge
-  - mantid-ornl
-  - mantid
-  - neutrons/label/rc
-  - oncat
-  - neutrons
-dependencies:
-  - anaconda-client
-  - boa
-  - conda-build
-  - conda-verify
-  - check-wheel-contents
-  - wheel
-  - mantidworkbench > 6.12.0
-  - pre-commit
-  - versioningit
-  - pylint=2.17.3
-  - pytest=7.2.1
-  - pytest-qt=4.2.0
-  - pytest-cov=4.0.0
-  - qtpy!=2.4.2
-  - setuptools
-  - sphinx
-  - sphinx-rtd-theme
-  - python-build
-  - configupdater
-  - pyoncat
-  - pyoncatqt >=1.2.0
-  - gtk3
-  - libstdcxx-ng
diff --git a/pyproject.toml b/pyproject.toml
index bee5be63..14286e9e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -98,27 +98,33 @@ configupdater = "*"
 [tool.pixi.pypi-dependencies]
 shiver = { path = ".", editable = true }
 toml-cli = ">=0.7.0,<0.8"
-pyoncat = "*"
-configupdater = "*"
 
 [tool.pixi.environments]
-default = { features = ["package", "developer"], solve-group = "default" }
+default = { features = ["package", "developer","docs","test",], solve-group = "default" }
 
 [tool.pixi.feature.package.dependencies]
+#conda package
 anaconda-client = ">=1.13.0,<2"
 twine = ">=6.1.0,<7"
 versioningit = "*"
 hatch = "*"
+#python package
+pip = "*"
 
+#code analysis tools
 [tool.pixi.feature.developer.dependencies]
-pip = "*"
-versioningit = "*"
-pre-commit = "*"
 pip-audit = ">=2.9.0,<3"
+pre-commit = "*"
 pylint = "*"
+codecov = ">=2.1.13"
+
+#readthedocs
+[tool.pixi.feature.docs.dependencies]
 sphinx = ">=8"
 sphinx_rtd_theme = ">=3.0.1"
-codecov = ">=2.1.13"
+
+#pytest
+[tool.pixi.feature.test.dependencies]
 pytest = ">=8.4.1"
 pytest-qt = ">=4.4.0"
 pytest-cov = ">=6.2.1"

From f86b0c392567dc22cb7065d8ced5a54848d5be83 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 10:26:14 -0400
Subject: [PATCH 03/53] version update

---
 pyproject.toml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 14286e9e..b3f8652a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,8 +31,8 @@ method = "minor"
 
 [tool.versioningit.format]
 distance = "{next_version}.dev{distance}"
-dirty = "{version}+d{build_date:%Y%m%d}"
-distance-dirty = "{next_version}.dev{distance}+d{build_date:%Y%m%d%H%M}"
+dirty = "{version}.dev{distance}"
+distance-dirty = "{version}.dev{distance}"
 
 [tool.versioningit.write]
 file = "src/shiver/_version.py"
@@ -81,6 +81,12 @@ version = "0.0.0" # placeholder, can be updated by task sync-version
 [tool.pixi.package.build]
 backend = { name = "pixi-build-python", version = "0.1.*" }
 
+[tool.hatch.build.hooks.versioningit-onbuild]
+source-file = "src/shiver/_version.py"
+build-file = "shiver/_version.py"
+replacement = '{base_version}'
+#artifacts = ["src/shiver/_version.py"]
+
 [tool.pixi.package.host-dependencies]
 hatchling = "*"
 versioningit = "*"

From 8a8e0df6b1663a3e4bb41288097f75daf4b1cdab Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 10:37:38 -0400
Subject: [PATCH 04/53] version update for dev

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index b3f8652a..91bd3ff4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,8 +31,8 @@ method = "minor"
 
 [tool.versioningit.format]
 distance = "{next_version}.dev{distance}"
-dirty = "{version}.dev{distance}"
-distance-dirty = "{version}.dev{distance}"
+dirty = "{next_version}.dev{distance}"
+distance-dirty = "{next_version}.dev{distance}"
 
 [tool.versioningit.write]
 file = "src/shiver/_version.py"

From c46780203bc89f82fe2f7ff96b5780e837dfc12f Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 11:35:42 -0400
Subject: [PATCH 05/53] hatch confs

---
 pyproject.toml | 36 ++++++++++++++++++++++--------------
 1 file changed, 22 insertions(+), 14 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 91bd3ff4..6b31eb59 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,24 +15,38 @@ documentation = "https://neutrons.github.io/Shiver/"
 
 [build-system]
 requires = [
-  "setuptools",
-   "wheel",
-   "toml",
-   "versioningit"
+  "hatchling",
+  "wheel",
+  "toml",
+  "versioningit"
 ]
-build-backend = "setuptools.build_meta"
+build-backend = "hatchling.build"
+
+[tool.hatch.version]
+source = "versioningit"
+
+[tool.hatch.build]
+artifacts = ["*.yml", "*.yaml", "*.ini", "*.gx", "*.json", "*.ui"]
+
+[tool.hatch.build.hooks.versioningit-onbuild]
+source-file = "src/shiver/_version.py"
+build-file = "shiver/_version.py"
+regex = '^\s*__version__\s*=\s*"(?P<version>[^"+\r\n]+)"'
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/shiver"]
 
 [tool.versioningit.vcs]
 method = "git"
-default-tag = "0.0.1"
+default-tag = "4.0.0"
 
 [tool.versioningit.next-version]
 method = "minor"
 
 [tool.versioningit.format]
 distance = "{next_version}.dev{distance}"
-dirty = "{next_version}.dev{distance}"
-distance-dirty = "{next_version}.dev{distance}"
+dirty = "{version}+d{build_date:%Y%m%d}"
+distance-dirty = "{next_version}.dev{distance}+d{build_date:%Y%m%d%H%M}"
 
 [tool.versioningit.write]
 file = "src/shiver/_version.py"
@@ -73,7 +87,6 @@ channels = [
   "oncat"
 ]
 
-
 [tool.pixi.package]
 name = "shiver"
 version = "0.0.0" # placeholder, can be updated by task sync-version
@@ -81,11 +94,6 @@ version = "0.0.0" # placeholder, can be updated by task sync-version
 [tool.pixi.package.build]
 backend = { name = "pixi-build-python", version = "0.1.*" }
 
-[tool.hatch.build.hooks.versioningit-onbuild]
-source-file = "src/shiver/_version.py"
-build-file = "shiver/_version.py"
-replacement = '{base_version}'
-#artifacts = ["src/shiver/_version.py"]
 
 [tool.pixi.package.host-dependencies]
 hatchling = "*"

From 01b79c0304851835bb725e98173dd163e09ff3af Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 11:41:43 -0400
Subject: [PATCH 06/53] setuptools back

---
 pyproject.toml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6b31eb59..81c5bd5f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,12 +15,12 @@ documentation = "https://neutrons.github.io/Shiver/"
 
 [build-system]
 requires = [
-  "hatchling",
+  "setuptools",
   "wheel",
   "toml",
   "versioningit"
 ]
-build-backend = "hatchling.build"
+build-backend = "setuptools.build_meta"
 
 [tool.hatch.version]
 source = "versioningit"
@@ -33,9 +33,6 @@ source-file = "src/shiver/_version.py"
 build-file = "shiver/_version.py"
 regex = '^\s*__version__\s*=\s*"(?P<version>[^"+\r\n]+)"'
 
-[tool.hatch.build.targets.wheel]
-packages = ["src/shiver"]
-
 [tool.versioningit.vcs]
 method = "git"
 default-tag = "4.0.0"

From 6f5c3d03671ecb308de80354b7a206672e74f6c2 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 11:44:16 -0400
Subject: [PATCH 07/53] hatcling regex

---
 pyproject.toml | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 81c5bd5f..fa404a7b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,12 +15,12 @@ documentation = "https://neutrons.github.io/Shiver/"
 
 [build-system]
 requires = [
-  "setuptools",
+  "hatchling",
   "wheel",
   "toml",
   "versioningit"
 ]
-build-backend = "setuptools.build_meta"
+build-backend = "hatchling.build"
 
 [tool.hatch.version]
 source = "versioningit"
@@ -31,7 +31,11 @@ artifacts = ["*.yml", "*.yaml", "*.ini", "*.gx", "*.json", "*.ui"]
 [tool.hatch.build.hooks.versioningit-onbuild]
 source-file = "src/shiver/_version.py"
 build-file = "shiver/_version.py"
-regex = '^\s*__version__\s*=\s*"(?P<version>[^"+\r\n]+)"'
+#regex = '^\s*__version__\s*=\s*"(?P<version>[^"+\r\n]+)"'
+
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/shiver"]
 
 [tool.versioningit.vcs]
 method = "git"

From 040c593ff8d51efebbc20cd294acaec950795dbc Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 12:00:07 -0400
Subject: [PATCH 08/53] hatchling back

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index fa404a7b..a0cb579e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -84,7 +84,6 @@ channels = [
   "mantid-ornl",
   "mantid",
   "neutrons",
-  "neutrons/label/rc",
   "oncat"
 ]
 

From 6d3112fae6ca806586f36a2302ef3af9ac509b94 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 12:22:20 -0400
Subject: [PATCH 09/53] versioning confs, setutools completely removed

---
 pyproject.toml | 27 +++++++++------------------
 1 file changed, 9 insertions(+), 18 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index a0cb579e..0021eca7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,6 +13,9 @@ homepage = "https://github.com/neutrons/Shiver/"
 repository = "https://github.com/neutrons/Shiver/"
 documentation = "https://neutrons.github.io/Shiver/"
 
+[project.gui-scripts]
+shiver = "shiver.shiver:gui"
+
 [build-system]
 requires = [
   "hatchling",
@@ -26,17 +29,18 @@ build-backend = "hatchling.build"
 source = "versioningit"
 
 [tool.hatch.build]
-artifacts = ["*.yml", "*.yaml", "*.ini", "*.gx", "*.json", "*.ui"]
+artifacts = ["*.yml", "*.yaml", "*.json"]
 
 [tool.hatch.build.hooks.versioningit-onbuild]
 source-file = "src/shiver/_version.py"
 build-file = "shiver/_version.py"
-#regex = '^\s*__version__\s*=\s*"(?P<version>[^"+\r\n]+)"'
-
 
 [tool.hatch.build.targets.wheel]
 packages = ["src/shiver"]
 
+[tool.versioningit.write]
+file = "src/shiver/_version.py"
+
 [tool.versioningit.vcs]
 method = "git"
 default-tag = "4.0.0"
@@ -46,22 +50,10 @@ method = "minor"
 
 [tool.versioningit.format]
 distance = "{next_version}.dev{distance}"
-dirty = "{version}+d{build_date:%Y%m%d}"
+dirty = "{version}"
 distance-dirty = "{next_version}.dev{distance}+d{build_date:%Y%m%d%H%M}"
 
-[tool.versioningit.write]
-file = "src/shiver/_version.py"
-
-[tool.setuptools.packages.find]
-where = ["src"]
-exclude = ["tests*", "DGS_SC_scripts*"]
-
-[tool.setuptools.package-data]
-"*" = ["*.yml","*.yaml","*.json"]
-
-[project.gui-scripts]
-shiver = "shiver.shiver:gui"
-
+#pylint
 [tool.pylint]
 max-line-length = 120
 disable = ["too-many-locals",
@@ -94,7 +86,6 @@ version = "0.0.0" # placeholder, can be updated by task sync-version
 [tool.pixi.package.build]
 backend = { name = "pixi-build-python", version = "0.1.*" }
 
-
 [tool.pixi.package.host-dependencies]
 hatchling = "*"
 versioningit = "*"

From 0ebb663f6dded255e864336727d391b0ae29b95d Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 14:13:28 -0400
Subject: [PATCH 10/53] distance updates

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0021eca7..93936828 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,7 +51,7 @@ method = "minor"
 [tool.versioningit.format]
 distance = "{next_version}.dev{distance}"
 dirty = "{version}"
-distance-dirty = "{next_version}.dev{distance}+d{build_date:%Y%m%d%H%M}"
+distance-dirty = "{next_version}.dev{distance}"
 
 #pylint
 [tool.pylint]

From 804294174c61a51bb7098bcc5297f1c44a74eb83 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 14:20:37 -0400
Subject: [PATCH 11/53] pixi lock ignored

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 93936828..29811604 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -63,7 +63,7 @@ disable = ["too-many-locals",
            "duplicate-code"
 ]
 extension-pkg-whitelist = ["PyQt5"]
-
+ignore = ["pixi.lock"]
 # ------------------ #
 # Pixi configuration #
 # ------------------ #

From 2a5f379dbb3c7d98282ea6153b546c830f1c0927 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 14:26:01 -0400
Subject: [PATCH 12/53] pixi lock file added

---
 .pre-commit-config.yaml |    1 +
 pixi.lock               | 6493 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 6494 insertions(+)
 create mode 100644 pixi.lock

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a04b68c3..190ea336 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -25,6 +25,7 @@ repos:
     rev: v2.4.1
     hooks:
     - id: codespell
+      exclude: pixi.lock
   - repo: local
     hooks:
     - id: pylint
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 00000000..6162e92d
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,6493 @@
+version: 6
+environments:
+  default:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    - url: https://prefix.dev/pixi-build-backends/
+    - url: https://conda.anaconda.org/mantid-ornl/
+    - url: https://conda.anaconda.org/mantid/
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+  license_family: MIT
+  purls: []
+  size: 89141
+  timestamp: 1641346969816
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.5-h3b0a872_7.conda
+  sha256: a4dc72c96848f764bb5a5176aa93dd1e9b9e52804137b99daeebba277b31ea10
+  md5: 3947a35e916fcc6b9825449affbf4214
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - krb5 >=1.21.3,<1.22.0a0
+  - libgcc >=13
+  - libsodium >=1.0.20,<1.0.21.0a0
+  - libstdcxx >=13
+  license: MPL-2.0
+  license_family: MOZILLA
+  purls: []
+  size: 335400
+  timestamp: 1731585026517
+- conda: https://conda.anaconda.org/conda-forge/noarch/zipp-3.23.0-pyhd8ed1ab_0.conda
+  sha256: 7560d21e1b021fd40b65bfb72f67945a3fcb83d78ad7ccf37b8b3165ec3b68ad
+  md5: df5e78d904988eb55042c0c97446079f
+  depends:
+  - python >=3.9
+  license: MIT
+  license_family: MIT
+  purls:
+  - pkg:pypi/zipp?source=hash-mapping
+  size: 22963
+  timestamp: 1749421737203
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda
+  sha256: 5d7c0e5f0005f74112a34a7425179f4eb6e73c92f5d109e6af4ddeca407c92ab
+  md5: c9f075ab2f33b3bbee9e62d4ad0a6cd8
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - libzlib 1.3.1 hb9d3cd8_2
+  license: Zlib
+  license_family: Other
+  purls: []
+  size: 92286
+  timestamp: 1727963153079
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.23.0-py310ha75aee5_2.conda
+  sha256: f9b76c2f8a0f96e656843553272e547170182f5b8aba1a6bcba28f7611d87c23
+  md5: f9254b5b0193982416b91edcb4b2676f
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - cffi >=1.11
+  - libgcc >=13
+  - python >=3.10,<3.11.0a0
+  - python_abi 3.10.* *_cp310
+  license: BSD-3-Clause
+  license_family: BSD
+  purls:
+  - pkg:pypi/zstandard?source=hash-mapping
+  size: 722119
+  timestamp: 1745869786772
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
+  sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb
+  md5: 6432cb5d4ac0046c3ac0a8a0f95842f9
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - libstdcxx >=13
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 567578
+  timestamp: 1742433379869

From c1385d5d91488abc945da2f9ce6f5f156f7cd847 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 14:48:40 -0400
Subject: [PATCH 13/53] ci actions with pixi and conda pg installation check

---
 .github/workflows/package.yml               |  38 +++++++
 .github/workflows/{actions.yml => test.yml} | 110 +++++++++++---------
 2 files changed, 100 insertions(+), 48 deletions(-)
 create mode 100644 .github/workflows/package.yml
 rename .github/workflows/{actions.yml => test.yml} (51%)

diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
new file mode 100644
index 00000000..68f11e85
--- /dev/null
+++ b/.github/workflows/package.yml
@@ -0,0 +1,38 @@
+name: Packaging and Deployment
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [qa, main]
+    tags: ["v*"]
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 100
+          fetch-tags: true
+          ref: ${{ github.ref }}
+
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.10
+        with:
+          pixi-version: v0.48.2
+
+      - name: Build conda package
+        run: pixi run conda-build
+
+      - name: Upload package to anaconda
+        if: startsWith(github.ref, 'refs/tags/v')
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+          IS_RC: ${{ contains(github.ref, 'rc') }}
+        run: |
+          # label is main or rc depending on the tag-name
+          CONDA_LABEL="main"
+          if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
+          echo pushing ${{ github.ref }} with label $CONDA_LABEL
+          pixi run anaconda upload --label $CONDA_LABEL --user neutrons shiver-*.conda
diff --git a/.github/workflows/actions.yml b/.github/workflows/test.yml
similarity index 51%
rename from .github/workflows/actions.yml
rename to .github/workflows/test.yml
index d1a24a1c..d0f4b89a 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/test.yml
@@ -14,10 +14,12 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v4
-    - uses: mamba-org/setup-micromamba@v2
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Setup Pixi
+      uses: prefix-dev/setup-pixi@v0.8.10
       with:
-        environment-file: environment.yml
+        pixi-version: v0.48.2
     - name: pylint
       run: pre-commit run -a pylint
     - name: Install shiver
@@ -29,54 +31,66 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
 
-  conda-build:
-    runs-on: ubuntu-latest
+  package:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 100
+          fetch-tags: true
+          ref: ${{ github.ref }}
+
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.10
+        with:
+          pixi-version: v0.48.2
+
+      - name: Build Conda package
+        run: pixi run conda-build
+
+      - name: upload conda package as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifact-conda-package
+          path: shiver-*.conda
+
+  conda-verify:
+    needs: tests
+    runs-on: ubuntu-24.04
     defaults:
       run:
-        shell: bash -l {0}
+        shell: bash -el {0}
     steps:
-    - name: Checkout
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 100
-        fetch-tags: true
-        ref: ${{ github.ref }}
-    - name: Micromamba
-      uses: mamba-org/setup-micromamba@v2
-      with:
-        environment-file: environment.yml
-        condarc: |
-          channels:
-            - conda-forge
-            - mantid-ornl
-            - neutrons/label/rc
-            - oncat
-    - name: Build python wheel
-      run: |
-        python -m build --wheel --no-isolation
-        check-wheel-contents dist/shiver-*.whl
-    - name: Build conda library
-      shell: bash -l {0}
-      run: |
-        # set up environment
-        cd conda.recipe
-        echo "versioningit $(versioningit ../)"
-        # build the package
-        CHANNELS="--channel conda-forge --channel mantid-ornl --channel neutrons/label/rc --channel oncat"
-        VERSION=$(versioningit ../) conda mambabuild $CHANNELS --output-folder . .
-        conda verify noarch/shiver*.tar.bz2
-    - name: Deploy to Anaconda
-      shell: bash -l {0}
-      if: startsWith(github.ref, 'refs/tags/v')
-      env:
-        ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-        IS_RC: ${{ contains(github.ref, 'rc') }}
-      run: |
-        # label is main or rc depending on the tag-name
-        CONDA_LABEL="main"
-        if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
-        echo pushing ${{ github.ref }} with label $CONDA_LABEL
-        anaconda upload --label $CONDA_LABEL conda.recipe/noarch/shiver*.tar.bz2
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+          ref: ${{ github.ref }}
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-name: test
+          init-shell: bash
+          create-args: >-
+            python=3.10
+
+      - name: Download conda package artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: artifact-conda-package
+          path: /tmp/local-channel/linux-64
+
+      - name: Install the package
+        run: |
+          micromamba install --yes -c conda-forge conda-build conda-index
+          python -m conda_index /tmp/local-channel
+          micromamba install --yes -c /tmp/local-channel -c mantid-ornl -c conda-forge shiver
+
+      - name: Verify the installation
+        run: python -c "import shiver"
 
   # trigger-deploy:
   #   runs-on: ubuntu-22.04

From 69c4dbe4870ab57c5e171bc5e44ef1dd4efb913b Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 14:54:14 -0400
Subject: [PATCH 14/53] conda build renaming

---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 29811604..a095f42f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -145,10 +145,10 @@ publish-pypi = { cmd = "twine upload dist/*", description = "Publish the package
   "build-pypi",
 ] }
 # Conda
-build-conda-command = { cmd = "pixi build", description = "Build the conda package command" }
-build-conda = { description = "Build the conda package", depends-on = [
+conda-build-command = { cmd = "pixi build", description = "Build the conda package command" }
+conda-build = { description = "Build the conda package", depends-on = [
   "sync-version",
-  "build-conda-command",
+  "conda-build-command",
   "reset-version",
 ] }
 clean-conda = { cmd = "rm shiver-*.conda", description = "Clean the conda build artifacts" }

From f7b1944b4b93524572123bf9094f51c9cbf6aaee Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 14:58:52 -0400
Subject: [PATCH 15/53] build conda command everywhere

---
 .github/workflows/package.yml | 2 +-
 .github/workflows/test.yml    | 4 ++--
 pixi.lock                     | 4 ++--
 pyproject.toml                | 6 +++---
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
index 68f11e85..24850e08 100644
--- a/.github/workflows/package.yml
+++ b/.github/workflows/package.yml
@@ -23,7 +23,7 @@ jobs:
           pixi-version: v0.48.2
 
       - name: Build conda package
-        run: pixi run conda-build
+        run: pixi run build-conda
 
       - name: Upload package to anaconda
         if: startsWith(github.ref, 'refs/tags/v')
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d0f4b89a..5147a8ae 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -47,7 +47,7 @@ jobs:
           pixi-version: v0.48.2
 
       - name: Build Conda package
-        run: pixi run conda-build
+        run: pixi run build-conda
 
       - name: upload conda package as artifact
         uses: actions/upload-artifact@v4
@@ -85,7 +85,7 @@ jobs:
 
       - name: Install the package
         run: |
-          micromamba install --yes -c conda-forge conda-build conda-index
+          micromamba install --yes -c conda-forge build-conda conda-index
           python -m conda_index /tmp/local-channel
           micromamba install --yes -c /tmp/local-channel -c mantid-ornl -c conda-forge shiver
 
diff --git a/pixi.lock b/pixi.lock
index 6162e92d..d18c494a 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -5459,8 +5459,8 @@ packages:
   timestamp: 1733301007770
 - pypi: ./
   name: shiver
-  version: 1.7.0.dev13
-  sha256: 7f9662a3710bd16a63449c7bd365c9211baae8fb6ba1249859f451ff79209343
+  version: 1.7.0.dev16
+  sha256: b35053de31b1231cd4d86acc21a69423d44f30f74655a89171349e5b62ba089d
   requires_python: '>=3.10'
   editable: true
 - conda: https://conda.anaconda.org/conda-forge/linux-64/sip-6.7.12-py310hc6cd4ac_0.conda
diff --git a/pyproject.toml b/pyproject.toml
index a095f42f..29811604 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -145,10 +145,10 @@ publish-pypi = { cmd = "twine upload dist/*", description = "Publish the package
   "build-pypi",
 ] }
 # Conda
-conda-build-command = { cmd = "pixi build", description = "Build the conda package command" }
-conda-build = { description = "Build the conda package", depends-on = [
+build-conda-command = { cmd = "pixi build", description = "Build the conda package command" }
+build-conda = { description = "Build the conda package", depends-on = [
   "sync-version",
-  "conda-build-command",
+  "build-conda-command",
   "reset-version",
 ] }
 clean-conda = { cmd = "rm shiver-*.conda", description = "Clean the conda build artifacts" }

From a5c46d3850be152f0c6c57de2a65a2a3e43ada05 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 15:03:39 -0400
Subject: [PATCH 16/53] update lockfiles action

---
 .github/workflows/update-lockfiles.yml | 36 ++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 .github/workflows/update-lockfiles.yml

diff --git a/.github/workflows/update-lockfiles.yml b/.github/workflows/update-lockfiles.yml
new file mode 100644
index 00000000..e5fbea90
--- /dev/null
+++ b/.github/workflows/update-lockfiles.yml
@@ -0,0 +1,36 @@
+name: Update lockfiles
+
+permissions:
+  contents: write
+  pull-requests: write
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: 0 5 1 * *
+
+jobs:
+  pixi-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4.2.2
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.8.10
+        with:
+          run-install: false
+      - name: Update lockfiles
+        run: |
+          set -o pipefail
+          pixi update --json | pixi exec pixi-diff-to-markdown >> diff.md
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: Update pixi lockfile
+          title: Update pixi lockfile
+          body-path: diff.md
+          branch: update-pixi
+          base: next  # change this to the default branch of your repository
+          labels: pixi
+          delete-branch: true
+          add-paths: pixi.lock

From 4d050793f482c7c85ef3484560b74a737d58b1f5 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 15:05:52 -0400
Subject: [PATCH 17/53] pixi lock

---
 pixi.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index d18c494a..a1ba5d47 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -5459,8 +5459,8 @@ packages:
   timestamp: 1733301007770
 - pypi: ./
   name: shiver
-  version: 1.7.0.dev16
-  sha256: b35053de31b1231cd4d86acc21a69423d44f30f74655a89171349e5b62ba089d
+  version: 1.7.0.dev18
+  sha256: 7f9662a3710bd16a63449c7bd365c9211baae8fb6ba1249859f451ff79209343
   requires_python: '>=3.10'
   editable: true
 - conda: https://conda.anaconda.org/conda-forge/linux-64/sip-6.7.12-py310hc6cd4ac_0.conda

From a152d4b0518a5157baf065c54adf3dc1785c4520 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 15:30:06 -0400
Subject: [PATCH 18/53] pylint errors fixed

---
 pyproject.toml                           | 3 +++
 src/shiver/models/histogram.py           | 4 +++-
 src/shiver/views/histogram_parameters.py | 2 +-
 3 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 29811604..911a5669 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,10 +60,13 @@ disable = ["too-many-locals",
            "too-many-statements",
            "too-many-instance-attributes",
            "too-many-arguments",
+           "too-many-positional-arguments",
            "duplicate-code"
 ]
 extension-pkg-whitelist = ["PyQt5"]
 ignore = ["pixi.lock"]
+
+
 # ------------------ #
 # Pixi configuration #
 # ------------------ #
diff --git a/src/shiver/models/histogram.py b/src/shiver/models/histogram.py
index ad6fa148..7d98b4a8 100644
--- a/src/shiver/models/histogram.py
+++ b/src/shiver/models/histogram.py
@@ -67,7 +67,9 @@ def load(self, filename, ws_type):
             logger.error(f"Unsupported workspace type {ws_type} for {filename}")
 
         endrange = 100
-        progress = Progress(load, start=0.0, end=1.0, nreports=endrange)
+        progress = Progress(
+            load, start=0.0, end=1.0, nreports=endrange  # pylint: disable=possibly-used-before-assignment
+        )
         progress.report(info_step)
         alg_obs = FileLoadingObserver(self, filename, ws_type, ws_name)
         self.algorithms_observers.add(alg_obs)
diff --git a/src/shiver/views/histogram_parameters.py b/src/shiver/views/histogram_parameters.py
index 54989d42..75a7f68a 100644
--- a/src/shiver/views/histogram_parameters.py
+++ b/src/shiver/views/histogram_parameters.py
@@ -873,7 +873,7 @@ def min_max_compare(self, cmin, cmax):
 
         else:
             # it should never be here
-            return
+            print("it should never be here")
 
     def min_max_checked(self, cmin, cmax):
         """Ensure Minimum and Maximum value pairs are:

From e453990ed27e45be0895b120ef563b53b4ece7b4 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 15:31:29 -0400
Subject: [PATCH 19/53] pixi lock update

---
 pixi.lock | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index a1ba5d47..840959db 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -5459,8 +5459,8 @@ packages:
   timestamp: 1733301007770
 - pypi: ./
   name: shiver
-  version: 1.7.0.dev18
-  sha256: 7f9662a3710bd16a63449c7bd365c9211baae8fb6ba1249859f451ff79209343
+  version: 1.7.0.dev20
+  sha256: ec770057701f6cc0fc385581bc63edf0ef918bc61ee6d5f1e3e25ff4bc5a73f1
   requires_python: '>=3.10'
   editable: true
 - conda: https://conda.anaconda.org/conda-forge/linux-64/sip-6.7.12-py310hc6cd4ac_0.conda

From 3fb36ba71ca3b74008e7217d911e278d12747a7c Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 16:09:42 -0400
Subject: [PATCH 20/53] pixi run added

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 5147a8ae..42cb28c6 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -21,7 +21,7 @@ jobs:
       with:
         pixi-version: v0.48.2
     - name: pylint
-      run: pre-commit run -a pylint
+      run: pixi run pre-commit run -a pylint
     - name: Install shiver
       run: python -m pip install -e .
     - name: Run tests

From 160d2ea68a6f9c4939e82d89bf85d98e74ee678e Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 16:21:59 -0400
Subject: [PATCH 21/53] audit added

---
 .github/workflows/test.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 42cb28c6..8d308355 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -22,10 +22,12 @@ jobs:
         pixi-version: v0.48.2
     - name: pylint
       run: pixi run pre-commit run -a pylint
+    - name: Python package security audit
+      run: pixi run audit-deps
     - name: Install shiver
-      run: python -m pip install -e .
+      run: pixi run python -m pip install -e .
     - name: Run tests
-      run: xvfb-run --server-args="-screen 0 1920x1080x24" -a python -m pytest --cov=src --cov-report=xml --cov-report=term
+      run: pixi run xvfb-run --server-args="-screen 0 1920x1080x24" -a python -m pytest --cov=src --cov-report=xml --cov-report=term
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v5
       with:

From 8cd758e630b1151ae528d2c40db5ed70d03a1342 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 16:24:04 -0400
Subject: [PATCH 22/53] conda verify needs package

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 8d308355..33a60deb 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -58,7 +58,7 @@ jobs:
           path: shiver-*.conda
 
   conda-verify:
-    needs: tests
+    needs: package
     runs-on: ubuntu-24.04
     defaults:
       run:

From 9efcc567396ed96833968d1791594566ebb16361 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 16:25:08 -0400
Subject: [PATCH 23/53] audit removed

---
 .github/workflows/test.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 33a60deb..a070f93b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -22,8 +22,6 @@ jobs:
         pixi-version: v0.48.2
     - name: pylint
       run: pixi run pre-commit run -a pylint
-    - name: Python package security audit
-      run: pixi run audit-deps
     - name: Install shiver
       run: pixi run python -m pip install -e .
     - name: Run tests

From b72c90b171993255546e5a866f9f79355949340a Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 16:28:14 -0400
Subject: [PATCH 24/53] readthedocs changes

---
 .readthedocs.yaml | 27 ++++++++++++---------------
 1 file changed, 12 insertions(+), 15 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index f57410c5..31588b02 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,19 +1,16 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: "ubuntu-24.04"
   tools:
-    python: "mambaforge-4.10"
-
-python:
-  install:
-    - method: pip
-      path: .
-
-sphinx:
-  builder: html
-  configuration: docs/source/conf.py
-  fail_on_warning: true
-
-conda:
-  environment: environment.yml
+    python: "3.11"
+  jobs:
+    create_environment:
+      - asdf plugin add pixi
+      - asdf install pixi latest
+      - asdf global pixi latest
+    install:
+      - pixi install
+    build:
+      html:
+        - pixi run sphinx-build -T -b html docs $READTHEDOCS_OUTPUT/html

From 18b83be7233c0d57985e4a524b515d4d95d92f92 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 16:46:30 -0400
Subject: [PATCH 25/53] install

---
 .github/workflows/test.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a070f93b..dabe21e6 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -85,10 +85,7 @@ jobs:
 
       - name: Install the package
         run: |
-          micromamba install --yes -c conda-forge build-conda conda-index
-          python -m conda_index /tmp/local-channel
-          micromamba install --yes -c /tmp/local-channel -c mantid-ornl -c conda-forge shiver
-
+          micromamba install --yes  shiver*.conda
       - name: Verify the installation
         run: python -c "import shiver"
 

From b31281248be89217c5030723b6c7745370e62969 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 16:56:07 -0400
Subject: [PATCH 26/53] get package name

---
 .github/workflows/test.yml | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index dabe21e6..0235cd64 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -83,9 +83,22 @@ jobs:
           name: artifact-conda-package
           path: /tmp/local-channel/linux-64
 
+      - name: Get artifact file name
+        id: get_filename
+        run: |
+          echo "Files downloaded:"
+          ls /tmp/local-channel/linux-64
+          # Get the first file (assuming it's a .tar.bz2 or .conda package)
+          FILE_NAME=$(ls /tmp/local-channel/linux-64/*.tar.bz2 | head -n 1)
+          echo "Found file: $FILE_NAME"
+
+          # Save to GitHub Actions output
+          echo "conda_file=$FILE_NAME" >> "$GITHUB_OUTPUT"
+
       - name: Install the package
         run: |
-          micromamba install --yes  shiver*.conda
+          echo "Installation of " ${{ steps.get_filename.outputs.conda_file }}"
+          micromamba install --yes  ${{ steps.get_filename.outputs.conda_file }}"
       - name: Verify the installation
         run: python -c "import shiver"
 

From b880907c08f473261fae0ad06cff9dddfd0647cb Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 16:59:09 -0400
Subject: [PATCH 27/53] conda pkg extension

---
 .github/workflows/test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 0235cd64..edf53da5 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -88,8 +88,8 @@ jobs:
         run: |
           echo "Files downloaded:"
           ls /tmp/local-channel/linux-64
-          # Get the first file (assuming it's a .tar.bz2 or .conda package)
-          FILE_NAME=$(ls /tmp/local-channel/linux-64/*.tar.bz2 | head -n 1)
+          # Get the first file
+          FILE_NAME=$(ls /tmp/local-channel/linux-64/*.conda | head -n 1)
           echo "Found file: $FILE_NAME"
 
           # Save to GitHub Actions output

From 9d42995fbe0ed64e6bd0c8e293d8ac0b5bd3468f Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Tue, 1 Jul 2025 17:05:37 -0400
Subject: [PATCH 28/53] micromamba installation step

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index edf53da5..56596092 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -98,7 +98,7 @@ jobs:
       - name: Install the package
         run: |
           echo "Installation of " ${{ steps.get_filename.outputs.conda_file }}"
-          micromamba install --yes  ${{ steps.get_filename.outputs.conda_file }}"
+          micromamba install --channel-priority flexible --yes  ${{ steps.get_filename.outputs.conda_file }}"
       - name: Verify the installation
         run: python -c "import shiver"
 

From bc8408fffd6343f13c9dccf6b4fa7c608008dc70 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 11:06:32 -0400
Subject: [PATCH 29/53] runtimes dependencies added

---
 pixi.lock      | 4 ++--
 pyproject.toml | 8 +++++++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index 840959db..05cebbb7 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -5459,8 +5459,8 @@ packages:
   timestamp: 1733301007770
 - pypi: ./
   name: shiver
-  version: 1.7.0.dev20
-  sha256: ec770057701f6cc0fc385581bc63edf0ef918bc61ee6d5f1e3e25ff4bc5a73f1
+  version: 1.7.0.dev30
+  sha256: 5f52c58a73a944d1b74ad9d14b08a891a39b88b0c471e3091cd8ebfab9826e94
   requires_python: '>=3.10'
   editable: true
 - conda: https://conda.anaconda.org/conda-forge/linux-64/sip-6.7.12-py310hc6cd4ac_0.conda
diff --git a/pyproject.toml b/pyproject.toml
index 911a5669..51f53121 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -94,9 +94,14 @@ hatchling = "*"
 versioningit = "*"
 
 [tool.pixi.package.run-dependencies]
-toml = "*"
+toml = ">=0.10.2,<0.11"
+mantidworkbench = ">=6.12"
+pyoncat = ">=2.1"
+pyoncatqt =">=1.2.0"
+configupdater = "*"
 
 [tool.pixi.dependencies]
+# Conda package dependencies
 toml = ">=0.10.2,<0.11"
 mantidworkbench = ">=6.12"
 pyoncat = ">=2.1"
@@ -104,6 +109,7 @@ pyoncatqt =">=1.2.0"
 configupdater = "*"
 
 [tool.pixi.pypi-dependencies]
+# PyPI dependencies, including this package to allow local editable installs
 shiver = { path = ".", editable = true }
 toml-cli = ">=0.7.0,<0.8"
 

From 073a640307997f3ad585f84be14ec7845ec9d6b3 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 11:21:05 -0400
Subject: [PATCH 30/53] dependecies description, conda vreify steps

---
 .github/workflows/test.yml | 7 +++++--
 pixi.lock                  | 4 ++--
 pyproject.toml             | 7 +++++--
 3 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 56596092..ceaf494f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -97,10 +97,13 @@ jobs:
 
       - name: Install the package
         run: |
+          python -m conda_index /tmp/local-channel/
           echo "Installation of " ${{ steps.get_filename.outputs.conda_file }}"
-          micromamba install --channel-priority flexible --yes  ${{ steps.get_filename.outputs.conda_file }}"
+          micromamba install -c /tmp/local-channel -c conda-forge -c mantid-ornl -c mantid -c neutrons -c oncat --override-channels shiver
       - name: Verify the installation
-        run: python -c "import shiver"
+        run: |
+          python -c "import shiver"
+          shiver --version
 
   # trigger-deploy:
   #   runs-on: ubuntu-22.04
diff --git a/pixi.lock b/pixi.lock
index 05cebbb7..9ae44561 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -5459,8 +5459,8 @@ packages:
   timestamp: 1733301007770
 - pypi: ./
   name: shiver
-  version: 1.7.0.dev30
-  sha256: 5f52c58a73a944d1b74ad9d14b08a891a39b88b0c471e3091cd8ebfab9826e94
+  version: 1.7.0.dev31
+  sha256: 6ce8a1ad663a4c0bc40dab2a284a10b69047536fab009eccfdbc47de191f5a1f
   requires_python: '>=3.10'
   editable: true
 - conda: https://conda.anaconda.org/conda-forge/linux-64/sip-6.7.12-py310hc6cd4ac_0.conda
diff --git a/pyproject.toml b/pyproject.toml
index 51f53121..5bd86df7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -94,6 +94,7 @@ hatchling = "*"
 versioningit = "*"
 
 [tool.pixi.package.run-dependencies]
+#dependencies for the conda package - for shiver to run
 toml = ">=0.10.2,<0.11"
 mantidworkbench = ">=6.12"
 pyoncat = ">=2.1"
@@ -101,7 +102,7 @@ pyoncatqt =">=1.2.0"
 configupdater = "*"
 
 [tool.pixi.dependencies]
-# Conda package dependencies
+# Conda package dependencies for the local environment though pixi
 toml = ">=0.10.2,<0.11"
 mantidworkbench = ">=6.12"
 pyoncat = ">=2.1"
@@ -109,11 +110,13 @@ pyoncatqt =">=1.2.0"
 configupdater = "*"
 
 [tool.pixi.pypi-dependencies]
-# PyPI dependencies, including this package to allow local editable installs
+# PyPI dependencies for the local environment though pixi
+#including this package to allow local editable installs
 shiver = { path = ".", editable = true }
 toml-cli = ">=0.7.0,<0.8"
 
 [tool.pixi.environments]
+#environment definitions with feature dependencies
 default = { features = ["package", "developer","docs","test",], solve-group = "default" }
 
 [tool.pixi.feature.package.dependencies]

From 6f89be2f1b84f39b54a749ef3630c08fc465cac2 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 11:29:31 -0400
Subject: [PATCH 31/53] conda-build installation on CI

---
 .github/workflows/test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ceaf494f..14fd2b6f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -97,6 +97,7 @@ jobs:
 
       - name: Install the package
         run: |
+          micromamba install --yes -c conda-forge conda-build conda-index
           python -m conda_index /tmp/local-channel/
           echo "Installation of " ${{ steps.get_filename.outputs.conda_file }}"
           micromamba install -c /tmp/local-channel -c conda-forge -c mantid-ornl -c mantid -c neutrons -c oncat --override-channels shiver

From 802b753f2753a335eefb83ddf4725b559f189edb Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 11:34:51 -0400
Subject: [PATCH 32/53] test. yml typos

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 14fd2b6f..983408e5 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -99,7 +99,7 @@ jobs:
         run: |
           micromamba install --yes -c conda-forge conda-build conda-index
           python -m conda_index /tmp/local-channel/
-          echo "Installation of " ${{ steps.get_filename.outputs.conda_file }}"
+          echo "Installation of ${{ steps.get_filename.outputs.conda_file }}"
           micromamba install -c /tmp/local-channel -c conda-forge -c mantid-ornl -c mantid -c neutrons -c oncat --override-channels shiver
       - name: Verify the installation
         run: |

From a80d8cd06e08ed18af93c490c3681f3101bd6067 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 11:50:53 -0400
Subject: [PATCH 33/53] mplbackend added in github actions

---
 .github/workflows/test.yml | 4 +++-
 pixi.lock                  | 4 ++--
 pyproject.toml             | 2 ++
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 983408e5..bfa97da7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -102,7 +102,9 @@ jobs:
           echo "Installation of ${{ steps.get_filename.outputs.conda_file }}"
           micromamba install -c /tmp/local-channel -c conda-forge -c mantid-ornl -c mantid -c neutrons -c oncat --override-channels shiver
       - name: Verify the installation
-        run: |
+        env:
+          MPLBACKEND: Agg
+      run: |
           python -c "import shiver"
           shiver --version
 
diff --git a/pixi.lock b/pixi.lock
index 9ae44561..99b4020c 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -5459,8 +5459,8 @@ packages:
   timestamp: 1733301007770
 - pypi: ./
   name: shiver
-  version: 1.7.0.dev31
-  sha256: 6ce8a1ad663a4c0bc40dab2a284a10b69047536fab009eccfdbc47de191f5a1f
+  version: 1.7.0.dev34
+  sha256: 3b12a5ef6f5ad2474491f10cb2a39e91468c3488ec3c0a8ccab09afaca4a1e5e
   requires_python: '>=3.10'
   editable: true
 - conda: https://conda.anaconda.org/conda-forge/linux-64/sip-6.7.12-py310hc6cd4ac_0.conda
diff --git a/pyproject.toml b/pyproject.toml
index 5bd86df7..825e9ab5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,9 +4,11 @@ description = "Spectroscopy Histogram Visualizer for Event Reduction"
 dynamic = ["version"]
 requires-python = ">=3.10"
 dependencies = [
+    # Dependencies available from both PyPI and conda should be listed here
 ]
 readme = "README.md"
 license = { text = "GPL3.0" }
+keywords = ["neutrons", "Spectroscopy", "direct geometry"]
 
 [project.urls]
 homepage = "https://github.com/neutrons/Shiver/"

From 127d16ff21409af31fb7a369fd077040edb93f62 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 11:51:13 -0400
Subject: [PATCH 34/53] space fixed

---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index bfa97da7..72ced68d 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -104,7 +104,7 @@ jobs:
       - name: Verify the installation
         env:
           MPLBACKEND: Agg
-      run: |
+        run: |
           python -c "import shiver"
           shiver --version
 

From d73ea90eae7eaec08580b364f0355d5fb0352bb5 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 11:58:44 -0400
Subject: [PATCH 35/53] readthedocs point to config folder added

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 31588b02..dfed9f90 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -13,4 +13,4 @@ build:
       - pixi install
     build:
       html:
-        - pixi run sphinx-build -T -b html docs $READTHEDOCS_OUTPUT/html
+        - pixi run sphinx-build -T -b html docs/source $READTHEDOCS_OUTPUT/html

From 02020d30ea7c256788da6c653fd059396200358c Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 12:45:24 -0400
Subject: [PATCH 36/53] actions updated with publish step after verify

---
 .github/workflows/{test.yml => actions.yml} | 37 +++++++++++++++++++-
 .github/workflows/package.yml               | 38 ---------------------
 2 files changed, 36 insertions(+), 39 deletions(-)
 rename .github/workflows/{test.yml => actions.yml} (77%)
 delete mode 100644 .github/workflows/package.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/actions.yml
similarity index 77%
rename from .github/workflows/test.yml
rename to .github/workflows/actions.yml
index 72ced68d..b299ad52 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/actions.yml
@@ -16,16 +16,21 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v4
+
     - name: Setup Pixi
       uses: prefix-dev/setup-pixi@v0.8.10
       with:
         pixi-version: v0.48.2
+
     - name: pylint
       run: pixi run pre-commit run -a pylint
+
     - name: Install shiver
       run: pixi run python -m pip install -e .
+
     - name: Run tests
       run: pixi run xvfb-run --server-args="-screen 0 1920x1080x24" -a python -m pytest --cov=src --cov-report=xml --cov-report=term
+
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v5
       with:
@@ -91,7 +96,6 @@ jobs:
           # Get the first file
           FILE_NAME=$(ls /tmp/local-channel/linux-64/*.conda | head -n 1)
           echo "Found file: $FILE_NAME"
-
           # Save to GitHub Actions output
           echo "conda_file=$FILE_NAME" >> "$GITHUB_OUTPUT"
 
@@ -106,8 +110,39 @@ jobs:
           MPLBACKEND: Agg
         run: |
           python -c "import shiver"
+          echo " -- Shiver Version -- "
           shiver --version
 
+  publish:
+    runs-on: ubuntu-22.04
+    needs: [tests, conda-verify]
+    steps:
+      - name: Download conda package artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: artifact-conda-package
+          path: /tmp/local-channel/linux-64
+
+      - name: Get artifact conda package filename
+        run: |
+          echo "Files downloaded:"
+          ls /tmp/local-channel/linux-64
+          # Get the first file
+          FILE_NAME=$(ls /tmp/local-channel/linux-64/shiver-*.conda)
+          echo "Conda package file: $FILE_NAME"
+
+      - name: Upload package to anaconda
+        if: startsWith(github.ref, 'refs/tags/v')
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+          IS_RC: ${{ contains(github.ref, 'rc') }}
+        run: |
+          # label is main or rc depending on the tag-name
+          CONDA_LABEL="main"
+          if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
+          echo pushing ${{ github.ref }} with label $CONDA_LABEL
+          pixi run anaconda upload --label $CONDA_LABEL --user neutrons /tmp/local-channel/linux-64/shiver-*.conda
+
   # trigger-deploy:
   #   runs-on: ubuntu-22.04
   #   needs: [tests, conda-build]
diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
deleted file mode 100644
index 24850e08..00000000
--- a/.github/workflows/package.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-name: Packaging and Deployment
-
-on:
-  workflow_dispatch:
-  push:
-    branches: [qa, main]
-    tags: ["v*"]
-
-jobs:
-  linux:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 100
-          fetch-tags: true
-          ref: ${{ github.ref }}
-
-      - name: Setup Pixi
-        uses: prefix-dev/setup-pixi@v0.8.10
-        with:
-          pixi-version: v0.48.2
-
-      - name: Build conda package
-        run: pixi run build-conda
-
-      - name: Upload package to anaconda
-        if: startsWith(github.ref, 'refs/tags/v')
-        env:
-          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
-          IS_RC: ${{ contains(github.ref, 'rc') }}
-        run: |
-          # label is main or rc depending on the tag-name
-          CONDA_LABEL="main"
-          if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
-          echo pushing ${{ github.ref }} with label $CONDA_LABEL
-          pixi run anaconda upload --label $CONDA_LABEL --user neutrons shiver-*.conda

From b08c9bcf22f7ff32176b16125fa53e0158f7191f Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 12:54:36 -0400
Subject: [PATCH 37/53] comment

---
 .github/workflows/actions.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index b299ad52..952b84af 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -117,7 +117,7 @@ jobs:
     runs-on: ubuntu-22.04
     needs: [tests, conda-verify]
     steps:
-      - name: Download conda package artifact
+      - name: Download previous conda package artifact
         uses: actions/download-artifact@v4
         with:
           name: artifact-conda-package
@@ -129,7 +129,7 @@ jobs:
           ls /tmp/local-channel/linux-64
           # Get the first file
           FILE_NAME=$(ls /tmp/local-channel/linux-64/shiver-*.conda)
-          echo "Conda package file: $FILE_NAME"
+          echo "Conda package file to publish: $FILE_NAME"
 
       - name: Upload package to anaconda
         if: startsWith(github.ref, 'refs/tags/v')

From 37f0cdfa2ba35986e48951afcafd428c6c8053cb Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 13:22:53 -0400
Subject: [PATCH 38/53] documentation update, keywords, CI actions names

---
 .github/workflows/actions.yml | 12 ++++-----
 README.md                     | 48 +++++++++++++++++++++++++++--------
 pixi.lock                     |  4 +--
 pyproject.toml                |  2 +-
 4 files changed, 47 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 952b84af..76077441 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -8,7 +8,7 @@ on:
     tags: ['v*']
 
 jobs:
-  tests:
+  Testing-suite:
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -36,7 +36,7 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
 
-  package:
+  Conda-build:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout
@@ -60,8 +60,8 @@ jobs:
           name: artifact-conda-package
           path: shiver-*.conda
 
-  conda-verify:
-    needs: package
+  Conda-verify:
+    needs: Conda-build
     runs-on: ubuntu-24.04
     defaults:
       run:
@@ -113,9 +113,9 @@ jobs:
           echo " -- Shiver Version -- "
           shiver --version
 
-  publish:
+  Publish:
     runs-on: ubuntu-22.04
-    needs: [tests, conda-verify]
+    needs: [Testing-suite, Conda-verify]
     steps:
       - name: Download previous conda package artifact
         uses: actions/download-artifact@v4
diff --git a/README.md b/README.md
index b4bd597f..213a135c 100644
--- a/README.md
+++ b/README.md
@@ -4,21 +4,32 @@ Tool (desktop application) for allowing the examination of Time of Flight (ToF)
 
 ## Installation
 
-Create and activate conda environment for shiver development
+Create and activate a virtual environment with [Pixi](https://pixi.sh/).
+Prerequisites: Pixi installation e.g. for Linux
 
 ```bash
-conda env create
-# or
-mamba env create
+curl -fsSL https://pixi.sh/install.sh | sh
 
-conda activate shiver
 ```
 
-Install shiver (in editable mode) and start application
+Download the repository. Setup/Update the environment
 
 ```bash
-python -m pip install -e .
+pixi install
+```
+
+Enter the environment
+
+```bash
+pixi shell
+
+```
 
+The Shiver environment is activated and the application is ready to use.
+
+Start the application
+
+```bash
 shiver
 ```
 
@@ -33,6 +44,19 @@ s.show()
 
 ## For Contributors
 
+**Development/Deployment**
+
+
+---
+
+Any change to pyproject.toml, e.g. new dependencies, requires updating the pixi.lock file and including it in the commit.
+
+```bash
+
+pixi.lock
+
+```
+
 **Testing**
 
 ---
@@ -60,11 +84,15 @@ pre-commit install
 ---
 
 The repository runs automated tests on branches during Pull-Requests and on the main ones: next, main and qa. The jobs are described in .github/workflows/actions.yml:
-  * `Tests`. It includes pytest, pre-commit and code coverage tools
+  * `Testing suite`. It includes pytest, pre-commit and code coverage tools
+
+  * `Conda build`. A new conda package is built and uploaded in a github temporary location (servers).
+
+  * `Conda Verify`. The new conda package is installed in a test environment and checked, e.g. import shiver.
 
-  * `Conda build`. A new conda package is built and uploaded to Anaconda, depending upon git tags and authorized branches.
+  * `Publish`. The new conda package is uploaded in Anaconda Neutrons registry.
 
-  * `Trigger deploy`. Given that the two above jobs were successful, deployment is triggered.
+  * `Trigger deploy`. Given that the two above jobs were successful, deployment is triggered. (this is temporarily in comments)
 
 
 **Documentation Updates**
diff --git a/pixi.lock b/pixi.lock
index 99b4020c..24157287 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -5459,8 +5459,8 @@ packages:
   timestamp: 1733301007770
 - pypi: ./
   name: shiver
-  version: 1.7.0.dev34
-  sha256: 3b12a5ef6f5ad2474491f10cb2a39e91468c3488ec3c0a8ccab09afaca4a1e5e
+  version: 1.7.0.dev39
+  sha256: ad795ab721e811c44005e4530539be78d8330cb406a46aa5d0f91879822ae7fd
   requires_python: '>=3.10'
   editable: true
 - conda: https://conda.anaconda.org/conda-forge/linux-64/sip-6.7.12-py310hc6cd4ac_0.conda
diff --git a/pyproject.toml b/pyproject.toml
index 825e9ab5..02f9bfca 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ dependencies = [
 ]
 readme = "README.md"
 license = { text = "GPL3.0" }
-keywords = ["neutrons", "Spectroscopy", "direct geometry"]
+keywords = ["neutrons", "Spectroscopy", "data visualization"]
 
 [project.urls]
 homepage = "https://github.com/neutrons/Shiver/"

From e96c910701055e1a765a4ec06e6ed4883b61ef22 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 13:36:57 -0400
Subject: [PATCH 39/53] documentation update for pixi

---
 README.md                       |  2 +-
 docs/source/getting_started.rst | 42 +++++++++++++++++++++------------
 docs/source/usage.rst           |  8 +++----
 3 files changed, 32 insertions(+), 20 deletions(-)

diff --git a/README.md b/README.md
index 213a135c..87a2207f 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@ Tool (desktop application) for allowing the examination of Time of Flight (ToF)
 ## Installation
 
 Create and activate a virtual environment with [Pixi](https://pixi.sh/).
-Prerequisites: Pixi installation e.g. for Linux
+Prerequisites: Pixi installation e.g. for Linux:
 
 ```bash
 curl -fsSL https://pixi.sh/install.sh | sh
diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
index 1c501465..3cfb9da1 100644
--- a/docs/source/getting_started.rst
+++ b/docs/source/getting_started.rst
@@ -8,32 +8,36 @@ Getting Started
 Instructions for SHIVER development
 -----------------------------------
 
-Conda Configuration
+Pixi Configuration
 ```````````````````
-Create and activate conda environment for ``SHIVER``.
+Create and activate a virtual environment with [Pixi](https://pixi.sh/).
+Prerequisites: Pixi installation e.g. for Linux:
 
-.. code-block:: sh
+```bash
+curl -fsSL https://pixi.sh/install.sh | sh
 
-    conda env create --file environment.yml
-    # or
-    mamba env create --file environment.yml
+```
 
-    conda activate shiver
+Download the repository. Setup/Update the environment
 
-Install ``SHIVER`` (in `editable mode <https://pip.pypa.io/en/stable/cli/pip_install/#cmdoption-e>`_) and start application
+```bash
+pixi install
+```
 
-.. code-block:: sh
+Enter the environment
 
-    python -m pip install -e .
+```bash
+pixi shell
 
-    shiver
+```
 
-If it has been a while, once can update using
+The Shiver environment is activated and the application is ready to use.
 
-.. code-block:: sh
+Start the application
 
-    conda activate shiver
-    conda env update --file environment.yml --prune
+```bash
+shiver
+```
 
 To start ``SHIVER`` from within the Mantid workbench, start ``mantidworkbench`` then run the following in the
 ``IPython`` console
@@ -46,6 +50,14 @@ To start ``SHIVER`` from within the Mantid workbench, start ``mantidworkbench``
 
 **For Developers**
 
+Any change to pyproject.toml, e.g. new dependencies, requires updating the pixi.lock file and including it in the commit.
+
+```bash
+
+pixi.lock
+
+```
+
 To run all tests for ``SHIVER``
 
 .. code-block:: sh
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
index 14cb530d..1225d5bd 100644
--- a/docs/source/usage.rst
+++ b/docs/source/usage.rst
@@ -24,16 +24,16 @@ or as a package imported in Mantid workbench.
 Technologies
 ------------
 
-The project is written in Python (>=3.8). It is highly dependent on `Manitd <https://www.mantidproject.org>`_.
+The project is written in Python (>=3.10). It is highly dependent on `Mantid <https://www.mantidproject.org>`_.
 The Graphical User Interface (GUI) is based on `QtPy <https://github.com/spyder-ide/qtpy>`_ (version is defined by Mantid)
 
 
 Project Structure
 -----------------
 
-The main code of the project is at src/shiver and the tests are at ``tests/``
-folders. The project contains additional scripts at ``DGS_SC_scripts/`` folder,
-which are initial scripts that ``SHIVER`` was created around.
+The main code of the project is at src/shiver, the documentation is at ``docs/`` and the tests are at ``tests/``
+folders. The configurations for Pixi (pixi.lock, pyproject.toml) with pre-commit  and readthedocs configurations are located in the root directory of the repostitory.
+The project contains additional scripts at ``DGS_SC_scripts/`` folder, which are the initial scripts that ``SHIVER`` was created around.
 
 The code follows the `MVP (Model-View-Presenter) <https://developer.mantidproject.org/MVPDesign.html>`_ Thus,
 all current and future changes will follow this pattern.

From 94286cc75e25d05cc8e97c6e1018ca10132500d4 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 14:52:20 -0400
Subject: [PATCH 40/53] publish step update path and usage docs

---
 .github/workflows/actions.yml | 12 ++++++++----
 docs/source/usage.rst         |  2 +-
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 76077441..2f23a604 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -117,18 +117,22 @@ jobs:
     runs-on: ubuntu-22.04
     needs: [Testing-suite, Conda-verify]
     steps:
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.10
+        with:
+          pixi-version: v0.48.2
+
       - name: Download previous conda package artifact
         uses: actions/download-artifact@v4
         with:
           name: artifact-conda-package
-          path: /tmp/local-channel/linux-64
 
       - name: Get artifact conda package filename
         run: |
           echo "Files downloaded:"
-          ls /tmp/local-channel/linux-64
+          ls
           # Get the first file
-          FILE_NAME=$(ls /tmp/local-channel/linux-64/shiver-*.conda)
+          FILE_NAME=$(ls ./shiver-*.conda)
           echo "Conda package file to publish: $FILE_NAME"
 
       - name: Upload package to anaconda
@@ -141,7 +145,7 @@ jobs:
           CONDA_LABEL="main"
           if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
           echo pushing ${{ github.ref }} with label $CONDA_LABEL
-          pixi run anaconda upload --label $CONDA_LABEL --user neutrons /tmp/local-channel/linux-64/shiver-*.conda
+          pixi run anaconda upload --label $CONDA_LABEL --user neutrons ./shiver-*.conda
 
   # trigger-deploy:
   #   runs-on: ubuntu-22.04
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
index 1225d5bd..bce5fcd2 100644
--- a/docs/source/usage.rst
+++ b/docs/source/usage.rst
@@ -7,7 +7,7 @@ Installation
 ------------
 
 - Available as part of Mantid Workbench
-- From source code with `pip` and conda environment configuration
+- From source code with Pixi
 - As a conda package: `Shiver <https://anaconda.org/neutrons/shiver>`_
 
 Application Information

From 8eb75dc83ba3aaf948b5bd0e4adaafa459eb0672 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 15:05:21 -0400
Subject: [PATCH 41/53] publish step update checkout

---
 .github/workflows/actions.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 2f23a604..54073232 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -117,6 +117,9 @@ jobs:
     runs-on: ubuntu-22.04
     needs: [Testing-suite, Conda-verify]
     steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
       - name: Setup Pixi
         uses: prefix-dev/setup-pixi@v0.8.10
         with:

From 1165e944006de6cb963542c5ac5b2fcaf624c5c2 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Wed, 2 Jul 2025 16:55:11 -0400
Subject: [PATCH 42/53] include fetcing tags in publish step

---
 .github/workflows/actions.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index 54073232..cff74961 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -119,6 +119,10 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          fetch-depth: 100
+          fetch-tags: true
+          ref: ${{ github.ref }}
 
       - name: Setup Pixi
         uses: prefix-dev/setup-pixi@v0.8.10

From b9bad65e8b9db208bcb3108070ba1de9153b77c3 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 10:33:22 -0400
Subject: [PATCH 43/53] job name tests

---
 .github/workflows/actions.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index cff74961..ae93edfb 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -8,7 +8,8 @@ on:
     tags: ['v*']
 
 jobs:
-  Testing-suite:
+  tests:
+    name: Testing Suite
     runs-on: ubuntu-latest
     defaults:
       run:

From 0bdf97de9e644e3cff2d264d8ccc986b592c046c Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 10:43:50 -0400
Subject: [PATCH 44/53] changes from comments

---
 .github/workflows/actions.yml   |  2 +-
 docs/source/getting_started.rst | 37 ++++++++++++++-------------------
 pyproject.toml                  |  1 -
 3 files changed, 17 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
index ae93edfb..7fe2b6a9 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/actions.yml
@@ -116,7 +116,7 @@ jobs:
 
   Publish:
     runs-on: ubuntu-22.04
-    needs: [Testing-suite, Conda-verify]
+    needs: [tests, Conda-verify]
     steps:
       - name: Checkout
         uses: actions/checkout@v4
diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
index 3cfb9da1..79b64c1a 100644
--- a/docs/source/getting_started.rst
+++ b/docs/source/getting_started.rst
@@ -4,7 +4,6 @@ Getting Started
 .. _getting_started:
 
 
-
 Instructions for SHIVER development
 -----------------------------------
 
@@ -13,36 +12,34 @@ Pixi Configuration
 Create and activate a virtual environment with [Pixi](https://pixi.sh/).
 Prerequisites: Pixi installation e.g. for Linux:
 
-```bash
-curl -fsSL https://pixi.sh/install.sh | sh
+.. code-block:: bash
 
-```
+    curl -fsSL https://pixi.sh/install.sh | sh
 
 Download the repository. Setup/Update the environment
 
-```bash
-pixi install
-```
+.. code-block:: bash
+
+    pixi install
 
 Enter the environment
 
-```bash
-pixi shell
+.. code-block:: bash
 
-```
+    pixi shell
 
 The Shiver environment is activated and the application is ready to use.
 
 Start the application
 
-```bash
-shiver
-```
+.. code-block:: bash
+
+    shiver
 
 To start ``SHIVER`` from within the Mantid workbench, start ``mantidworkbench`` then run the following in the
 ``IPython`` console
 
-.. code-block:: sh
+.. code-block:: bash
 
     from shiver import Shiver
     s = Shiver()
@@ -52,15 +49,13 @@ To start ``SHIVER`` from within the Mantid workbench, start ``mantidworkbench``
 
 Any change to pyproject.toml, e.g. new dependencies, requires updating the pixi.lock file and including it in the commit.
 
-```bash
-
-pixi.lock
+.. code-block:: bash
 
-```
+    pixi.lock
 
 To run all tests for ``SHIVER``
 
-.. code-block:: sh
+.. code-block:: bash
 
     pytest
     #or
@@ -68,12 +63,12 @@ To run all tests for ``SHIVER``
 
 To run ``pre-commit`` manually
 
-.. code-block:: sh
+.. code-block:: bash
 
     pre-commit run --all-files
 
 Or to set the ``pre-commit`` hook before each ``git`` commit
 
-.. code-block:: sh
+.. code-block:: bash
 
     pre-commit install
diff --git a/pyproject.toml b/pyproject.toml
index 02f9bfca..5cacbe75 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,7 +55,6 @@ distance = "{next_version}.dev{distance}"
 dirty = "{version}"
 distance-dirty = "{next_version}.dev{distance}"
 
-#pylint
 [tool.pylint]
 max-line-length = 120
 disable = ["too-many-locals",

From 1af4381ff9b8d994a577a08444b80990972ca3ba Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 10:48:24 -0400
Subject: [PATCH 45/53] pixi lock check hook added

---
 .pre-commit-config.yaml | 7 ++++++-
 pixi.lock               | 4 ++--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 190ea336..ec3c018e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 exclude: "DGS_SC_scripts/.*|.*\\.mat$"
 
 ci:
-    skip: [pylint]
+    skip: [pylint, pixi-lock-check]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -38,3 +38,8 @@ repos:
           "-rn", # Only display messages
           "-sn", # Don't display the score
         ]
+    - id: pixi-lock-check
+      name: pixi-lock-check
+      entry: bash -c "pixi lock --check"
+      stage: pre-push
+      language: system
diff --git a/pixi.lock b/pixi.lock
index 24157287..775b9cd0 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -5459,8 +5459,8 @@ packages:
   timestamp: 1733301007770
 - pypi: ./
   name: shiver
-  version: 1.7.0.dev39
-  sha256: ad795ab721e811c44005e4530539be78d8330cb406a46aa5d0f91879822ae7fd
+  version: 1.7.0.dev46
+  sha256: aacccefcdc28cedcd24d84dbdc55b0025ef62ae15eafe2cbb8709a91c753579c
   requires_python: '>=3.10'
   editable: true
 - conda: https://conda.anaconda.org/conda-forge/linux-64/sip-6.7.12-py310hc6cd4ac_0.conda

From 3bb00d9634ab6d6a643690fe702966d244e0ee4f Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 12:13:07 -0400
Subject: [PATCH 46/53] github actions updates for consistency across projects

---
 .../{actions.yml => test_and_deploy.yml}      | 60 +++++++++----------
 1 file changed, 30 insertions(+), 30 deletions(-)
 rename .github/workflows/{actions.yml => test_and_deploy.yml} (80%)

diff --git a/.github/workflows/actions.yml b/.github/workflows/test_and_deploy.yml
similarity index 80%
rename from .github/workflows/actions.yml
rename to .github/workflows/test_and_deploy.yml
index 7fe2b6a9..b77d2178 100644
--- a/.github/workflows/actions.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -1,4 +1,4 @@
-name: CI
+name: Tests, Package, and Deployment
 
 on:
   workflow_dispatch:
@@ -7,6 +7,9 @@ on:
     branches: [next]
     tags: ['v*']
 
+env:
+  PKG_NAME: shiver
+
 jobs:
   tests:
     name: Testing Suite
@@ -37,7 +40,8 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
 
-  Conda-build:
+  build:
+    name: Conda build with Pixi
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout
@@ -53,16 +57,17 @@ jobs:
           pixi-version: v0.48.2
 
       - name: Build Conda package
-        run: pixi run build-conda
+        run: pixi run conda-build
 
       - name: upload conda package as artifact
         uses: actions/upload-artifact@v4
         with:
           name: artifact-conda-package
-          path: shiver-*.conda
+          path: ${{ env.PKG_NAME }}-*.conda
 
-  Conda-verify:
-    needs: Conda-build
+  conda-verify:
+    name: Conda Verify
+    needs: build
     runs-on: ubuntu-24.04
     defaults:
       run:
@@ -89,34 +94,29 @@ jobs:
           name: artifact-conda-package
           path: /tmp/local-channel/linux-64
 
-      - name: Get artifact file name
-        id: get_filename
-        run: |
-          echo "Files downloaded:"
-          ls /tmp/local-channel/linux-64
-          # Get the first file
-          FILE_NAME=$(ls /tmp/local-channel/linux-64/*.conda | head -n 1)
-          echo "Found file: $FILE_NAME"
-          # Save to GitHub Actions output
-          echo "conda_file=$FILE_NAME" >> "$GITHUB_OUTPUT"
-
       - name: Install the package
         run: |
           micromamba install --yes -c conda-forge conda-build conda-index
-          python -m conda_index /tmp/local-channel/
-          echo "Installation of ${{ steps.get_filename.outputs.conda_file }}"
-          micromamba install -c /tmp/local-channel -c conda-forge -c mantid-ornl -c mantid -c neutrons -c oncat --override-channels shiver
+          python -m conda_index /tmp/local-channel
+          micromamba install --yes -c /tmp/local-channel -c mantid-ornl -c conda-forge ${{ env.PKG_NAME }}
+
       - name: Verify the installation
-        env:
-          MPLBACKEND: Agg
         run: |
-          python -c "import shiver"
-          echo " -- Shiver Version -- "
-          shiver --version
-
-  Publish:
-    runs-on: ubuntu-22.04
-    needs: [tests, Conda-verify]
+          conda_version=$(micromamba list "${{ env.PKG_NAME }}" | awk -v pkg="${{ env.PKG_NAME }}" '$1 == pkg { print $2 }')
+          echo "Conda version: $conda_version"
+          python_version=$(python -c "import ${{ env.PKG_NAME }}; print(${{ env.PKG_NAME }}.__version__)")
+          echo "Python version: $python_version"
+          if [ "$conda_version" != "$python_version" ]; then
+            echo "Version mismatch!"
+            exit 1
+          else
+            echo "Versions match."
+          fi
+
+  publish:
+    name: Publish
+    runs-on: ubuntu-24.04
+    needs: [tests, conda-verify]
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -153,7 +153,7 @@ jobs:
           CONDA_LABEL="main"
           if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
           echo pushing ${{ github.ref }} with label $CONDA_LABEL
-          pixi run anaconda upload --label $CONDA_LABEL --user neutrons ./shiver-*.conda
+          pixi run anaconda upload --label $CONDA_LABEL --user neutrons ${{ env.PKG_NAME }}-*.conda
 
   # trigger-deploy:
   #   runs-on: ubuntu-22.04

From 894fcdae00db7b5c8c95f603dcb498b575085c68 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 12:14:13 -0400
Subject: [PATCH 47/53] readthedocs conf for os

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index dfed9f90..7e64895e 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,7 +1,7 @@
 version: 2
 
 build:
-  os: "ubuntu-24.04"
+  os: ubuntu-24.04
   tools:
     python: "3.11"
   jobs:

From cacf4fadf6829544b75d583bf56d7f79f64c3743 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 12:15:56 -0400
Subject: [PATCH 48/53] typos fixed

---
 .github/workflows/test_and_deploy.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index b77d2178..d2db64fe 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -57,7 +57,7 @@ jobs:
           pixi-version: v0.48.2
 
       - name: Build Conda package
-        run: pixi run conda-build
+        run: pixi run build-conda
 
       - name: upload conda package as artifact
         uses: actions/upload-artifact@v4

From 4a84be0779c4bae805f9078f9cdd04b2676bd56c Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 12:22:41 -0400
Subject: [PATCH 49/53] channels and other details are back

---
 .github/workflows/test_and_deploy.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index d2db64fe..61ac8b7c 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -98,9 +98,11 @@ jobs:
         run: |
           micromamba install --yes -c conda-forge conda-build conda-index
           python -m conda_index /tmp/local-channel
-          micromamba install --yes -c /tmp/local-channel -c mantid-ornl -c conda-forge ${{ env.PKG_NAME }}
+          micromamba install -c /tmp/local-channel -c conda-forge -c mantid-ornl -c mantid -c neutrons -c oncat ${{ env.PKG_NAME }}
 
       - name: Verify the installation
+        env:
+          MPLBACKEND: Agg
         run: |
           conda_version=$(micromamba list "${{ env.PKG_NAME }}" | awk -v pkg="${{ env.PKG_NAME }}" '$1 == pkg { print $2 }')
           echo "Conda version: $conda_version"

From eea472553dad5cdd80ab0a9382a9b351a0fc7b89 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 12:39:41 -0400
Subject: [PATCH 50/53] publish setp skipped for untagged commits

---
 .github/workflows/test_and_deploy.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 61ac8b7c..ac7908f7 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -119,6 +119,7 @@ jobs:
     name: Publish
     runs-on: ubuntu-24.04
     needs: [tests, conda-verify]
+    if: startsWith(github.ref, 'refs/tags/v')
     steps:
       - name: Checkout
         uses: actions/checkout@v4

From 705b4e6be8ccfaa8d013434df756c78eb69f0e80 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 12:47:36 -0400
Subject: [PATCH 51/53] extra check removed

---
 .github/workflows/test_and_deploy.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index ac7908f7..4746c354 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -147,7 +147,6 @@ jobs:
           echo "Conda package file to publish: $FILE_NAME"
 
       - name: Upload package to anaconda
-        if: startsWith(github.ref, 'refs/tags/v')
         env:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           IS_RC: ${{ contains(github.ref, 'rc') }}

From c584283ab80195e81ebf4eeac1b498ab7cec00ed Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 13:27:02 -0400
Subject: [PATCH 52/53] docs, commandsupdates

---
 .github/workflows/test_and_deploy.yml |   2 +-
 docs/Makefile                         |  21 --
 docs/make.bat                         |  37 --
 pixi.lock                             | 509 ++------------------------
 pyproject.toml                        |  63 ++--
 5 files changed, 66 insertions(+), 566 deletions(-)
 delete mode 100644 docs/Makefile
 delete mode 100644 docs/make.bat

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 4746c354..da4a383e 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -57,7 +57,7 @@ jobs:
           pixi-version: v0.48.2
 
       - name: Build Conda package
-        run: pixi run build-conda
+        run: pixi run conda-build
 
       - name: upload conda package as artifact
         uses: actions/upload-artifact@v4
diff --git a/docs/Makefile b/docs/Makefile
deleted file mode 100644
index 9d29d715..00000000
--- a/docs/Makefile
+++ /dev/null
@@ -1,21 +0,0 @@
-# Purpose: Convenience scripts to simplify some common Sphinx operations, such as rendering the content.
-
-# Minimal makefile for Sphinx documentation
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
-BUILDDIR      = build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/make.bat b/docs/make.bat
deleted file mode 100644
index 5a41d8d3..00000000
--- a/docs/make.bat
+++ /dev/null
@@ -1,37 +0,0 @@
-REM Purpose: Convenience scripts to simplify some common Sphinx operations, such as rendering the content.
-
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
diff --git a/pixi.lock b/pixi.lock
index 775b9cd0..a418943d 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -14,14 +14,12 @@ environments:
       linux-64:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
-      - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/adwaita-icon-theme-48.1-unix_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/alabaster-1.0.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/anaconda-cli-base-0.5.2-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/anaconda-client-1.13.0-pyh29332c3_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.9.0-pyh29332c3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/astroid-3.3.10-py310hff52083_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-atk-2.38.0-h0630a04_3.tar.bz2
@@ -30,8 +28,6 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.3.0-pyh71513ae_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/babel-2.17.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/backports-1.0-pyhd8ed1ab_5.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/backports.tarfile-1.2.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/blinker-1.9.0-pyhff2d567_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/boolean.py-5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hb9d3cd8_3.conda
@@ -48,8 +44,8 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-1.17.1-py310h8deb56e_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cfgv-3.3.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.2-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/check-wheel-contents-0.6.2-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/click-8.2.1-pyh707e725_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/cmarkgfm-2024.11.20-py310ha75aee5_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/codecov-2.1.13-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/comm-0.2.2-pyhd8ed1ab_1.conda
@@ -58,7 +54,6 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/configupdater-3.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.3.2-py310h3788b33_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/coverage-7.9.1-py310h89163eb_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.10.18-py310hd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/cryptography-45.0.4-py310h6c63255_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cyclonedx-python-lib-9.1.0-pyh29332c3_0.conda
@@ -71,7 +66,6 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.3.9-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/docutils-0.21.2-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/double-conversion-3.3.1-h5888daf_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/editables-0.5-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/elfutils-0.192-h7f4e02f_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/epoxy-1.5.10-h166bdaf_1.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/euphonic-1.4.4-py310hf462985_0.conda
@@ -107,23 +101,16 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.24.11-h651a532_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gstreamer-1.24.11-hc37bda9_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/gtk3-3.24.43-h0c6a113_5.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/h11-0.16.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/h2-4.2.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/h5py-3.14.0-nompi_py310hea1e86d_100.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-11.2.1-h3beb420_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/hatch-1.14.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/hatchling-1.27.0-pypyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf4-4.2.15-h2a13503_7.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/hdf5-1.14.6-nompi_h2d575fe_101.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/hicolor-icon-theme-0.17-ha770c72_2.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/hpack-4.1.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/html5lib-1.1-pyhd8ed1ab_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/httpcore-1.0.9-pyh29332c3_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/httpx-0.28.1-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/hyperframe-6.1.0-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/hyperlink-21.0.0-pyh29332c3_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/id-1.5.0-pyh29332c3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/identify-2.6.12-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/idna-3.10-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/imagesize-1.4.1-pyhd8ed1ab_0.tar.bz2
@@ -135,12 +122,8 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.29.5-pyh3099207_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/ipython-8.37.0-pyh8f84b5b_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/isort-6.0.1-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.classes-3.4.0-pyhd8ed1ab_2.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.context-6.0.1-pyhd8ed1ab_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.functools-4.1.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/jasper-4.2.5-h1920b20_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jedi-0.19.2-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/jeepney-0.9.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/jemalloc-5.2.0-he1b5a44_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.6-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/joblib-1.5.1-pyhd8ed1ab_0.conda
@@ -150,7 +133,6 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.6.3-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/jupyter_core-5.8.1-pyh31011fe_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/jxrlib-1.1-hd590300_3.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/keyring-25.6.0-pyha804496_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/kiwisolver-1.4.7-py310h3788b33_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda
@@ -257,7 +239,6 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.1.7-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mccabe-0.7.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/more-itertools-10.7.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/mpg123-1.32.9-hc50e24c_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/msgpack-python-1.1.1-py310h3788b33_0.conda
       - conda: https://conda.anaconda.org/mantid/noarch/mslice-2.11-pyh6af92e8_0.tar.bz2
@@ -269,7 +250,6 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.6.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/nettle-3.10.1-h4a9d5aa_0.conda
-      - conda: https://conda.anaconda.org/conda-forge/linux-64/nh3-0.2.21-py39h7c48542_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/nodeenv-1.9.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/nspr-4.36-h5888daf_0.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/nss-3.113-h159eef7_0.conda
@@ -285,7 +265,6 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pango-1.56.3-h9ac818e_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/parso-0.8.4-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/pathspec-0.12.1-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.44-hc749103_2.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/pexpect-4.9.0-pyhd8ed1ab_1.conda
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-- conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.classes-3.4.0-pyhd8ed1ab_2.conda
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-- conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.context-6.0.1-pyhd8ed1ab_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/noarch/jaraco.functools-4.1.0-pyhd8ed1ab_0.conda
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-- conda: https://conda.anaconda.org/conda-forge/noarch/jeepney-0.9.0-pyhd8ed1ab_0.conda
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-  size: 40015
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/jemalloc-5.2.0-he1b5a44_0.tar.bz2
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   md5: 56dc9bbd462a55a19eddb4809ab82612
@@ -2322,25 +2058,6 @@ packages:
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   size: 239104
   timestamp: 1703333860145
-- conda: https://conda.anaconda.org/conda-forge/noarch/keyring-25.6.0-pyha804496_0.conda
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-  depends:
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-  - importlib_resources
-  - jaraco.classes
-  - jaraco.context
-  - jaraco.functools
-  - jeepney >=0.4.2
-  - python >=3.9
-  - secretstorage >=3.2
-  license: MIT
-  license_family: MIT
-  purls:
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
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@@ -3763,17 +3480,6 @@ packages:
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   size: 14465
   timestamp: 1733255681319
-- conda: https://conda.anaconda.org/conda-forge/noarch/more-itertools-10.7.0-pyhd8ed1ab_0.conda
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-  size: 61359
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 - conda: https://conda.anaconda.org/conda-forge/linux-64/mpg123-1.32.9-hc50e24c_0.conda
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@@ -3919,24 +3625,6 @@ packages:
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-- conda: https://conda.anaconda.org/conda-forge/linux-64/nh3-0.2.21-py39h7c48542_2.conda
-  noarch: python
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-  - _python_abi3_support 1.*
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-  constrains:
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-  size: 624208
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 - conda: https://conda.anaconda.org/conda-forge/noarch/nodeenv-1.9.1-pyhd8ed1ab_1.conda
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   md5: 7ba3f09fceae6a120d664217e58fe686
@@ -4153,17 +3841,6 @@ packages:
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   size: 75295
   timestamp: 1733271352153
-- conda: https://conda.anaconda.org/conda-forge/noarch/pathspec-0.12.1-pyhd8ed1ab_1.conda
-  sha256: 9f64009cdf5b8e529995f18e03665b03f5d07c0b17445b8badef45bde76249ee
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-  license: MPL-2.0
-  license_family: MOZILLA
-  purls:
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-  size: 41075
-  timestamp: 1733233471940
 - conda: https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.44-hc749103_2.conda
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   md5: 31614c73d7b103ef76faa4d83d261d34
@@ -4869,16 +4546,6 @@ packages:
   - pkg:pypi/fastjsonschema?source=hash-mapping
   size: 226259
   timestamp: 1733236073335
-- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.10.18-hd8ed1ab_0.conda
-  sha256: 202221969a5fc255ecc30a0983e16bf08cb8dba36f82c5ac8271cfb92166a490
-  md5: a40e3a920f2c46f94e027bd599b88b17
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-  - python_abi * *_cp310
-  license: Python-2.0
-  purls: []
-  size: 50472
-  timestamp: 1749048192916
 - conda: https://conda.anaconda.org/conda-forge/noarch/python_abi-3.10-7_cp310.conda
   build_number: 7
   sha256: 1316c66889313d9caebcfa5d5e9e6af25f8ba09396fc1bc196a08a3febbbabb8
@@ -5265,21 +4932,6 @@ packages:
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   size: 282480
   timestamp: 1740379431762
-- conda: https://conda.anaconda.org/conda-forge/noarch/readme_renderer-44.0-pyhd8ed1ab_1.conda
-  sha256: 66f3adf6aaabf977cfcc22cb65607002b1de4a22bc9fac7be6bb774bc6f85a3a
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-  - docutils >=0.21.2
-  - nh3 >=0.2.14
-  - pygments >=2.5.1
-  - python >=3.9
-  license: Apache-2.0
-  license_family: APACHE
-  purls:
-  - pkg:pypi/readme-renderer?source=hash-mapping
-  size: 17481
-  timestamp: 1734339765256
 - conda: https://conda.anaconda.org/conda-forge/noarch/referencing-0.36.2-pyh29332c3_0.conda
   sha256: e20909f474a6cece176dfc0dc1addac265deb5fa92ea90e975fbca48085b20c3
   md5: 9140f1c09dd5489549c6a33931b943c7
@@ -5341,17 +4993,6 @@ packages:
   - pkg:pypi/requests-toolbelt?source=hash-mapping
   size: 44285
   timestamp: 1733734886897
-- conda: https://conda.anaconda.org/conda-forge/noarch/rfc3986-2.0.0-pyhd8ed1ab_1.conda
-  sha256: d617373ba1a5108336cb87754d030b9e384dcf91796d143fa60fe61e76e5cfb0
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-  license: Apache-2.0
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-  purls:
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-  size: 38028
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 - conda: https://conda.anaconda.org/conda-forge/noarch/rich-14.0.0-pyh29332c3_0.conda
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@@ -5406,21 +5047,6 @@ packages:
   - pkg:pypi/scipy?source=hash-mapping
   size: 16417101
   timestamp: 1739791865060
-- conda: https://conda.anaconda.org/conda-forge/linux-64/secretstorage-3.3.3-py310hff52083_3.conda
-  sha256: 6e5de234e690eda6bc09cea8db32344539c80e3d35daa7fda2bd9f8c1007532f
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-  - cryptography
-  - dbus
-  - jeepney >=0.6
-  - python >=3.10,<3.11.0a0
-  - python_abi 3.10.* *_cp310
-  license: BSD-3-Clause
-  license_family: BSD
-  purls:
-  - pkg:pypi/secretstorage?source=hash-mapping
-  size: 27103
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 - conda: https://conda.anaconda.org/conda-forge/noarch/seekpath-2.1.0-pyhd8ed1ab_1.conda
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   md5: 3e76fbd9c326b57ca42e3fc257582cec
@@ -5459,8 +5085,8 @@ packages:
   timestamp: 1733301007770
 - pypi: ./
   name: shiver
-  version: 1.7.0.dev46
-  sha256: aacccefcdc28cedcd24d84dbdc55b0025ef62ae15eafe2cbb8709a91c753579c
+  version: 1.7.0.dev53
+  sha256: c264e1e9dd9658880d3935935307e92e56739c5d5a8728095817b06e769a65b5
   requires_python: '>=3.10'
   editable: true
 - conda: https://conda.anaconda.org/conda-forge/linux-64/sip-6.7.12-py310hc6cd4ac_0.conda
@@ -5491,17 +5117,6 @@ packages:
   - pkg:pypi/six?source=hash-mapping
   size: 16385
   timestamp: 1733381032766
-- conda: https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.1-pyhd8ed1ab_1.conda
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-  md5: bf7a226e58dfb8346c70df36065d86c9
-  depends:
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-  license: Apache-2.0
-  license_family: Apache
-  purls:
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-  size: 15019
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 - conda: https://conda.anaconda.org/conda-forge/noarch/snowballstemmer-3.0.1-pyhd8ed1ab_0.conda
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@@ -5749,17 +5364,6 @@ packages:
   - pkg:pypi/tomli?source=hash-mapping
   size: 19167
   timestamp: 1733256819729
-- conda: https://conda.anaconda.org/conda-forge/noarch/tomli-w-1.2.0-pyhd8ed1ab_0.conda
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-  license: MIT
-  license_family: MIT
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-  size: 12680
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 - conda: https://conda.anaconda.org/conda-forge/noarch/tomlkit-0.13.3-pyha770c72_0.conda
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@@ -5818,39 +5422,6 @@ packages:
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   size: 110051
   timestamp: 1733367480074
-- conda: https://conda.anaconda.org/conda-forge/noarch/trove-classifiers-2025.5.9.12-pyhd8ed1ab_0.conda
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-  license: Apache-2.0
-  license_family: Apache
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-  timestamp: 1746817031708
-- conda: https://conda.anaconda.org/conda-forge/noarch/twine-6.1.0-pyh29332c3_0.conda
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-  - importlib-metadata >=3.6
-  - keyring >=15.1
-  - packaging >=24.0
-  - python >=3.9
-  - readme_renderer >=35.0
-  - requests >=2.20
-  - requests-toolbelt >=0.8.0,!=0.9.0
-  - rfc3986 >=1.4.0
-  - rich >=12.0.0
-  - urllib3 >=1.26.0
-  - python
-  license: Apache-2.0
-  license_family: APACHE
-  purls:
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 - conda: https://conda.anaconda.org/conda-forge/noarch/typer-0.16.0-pyh167b9f4_0.conda
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@@ -5992,31 +5563,6 @@ packages:
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   size: 101735
   timestamp: 1750271478254
-- conda: https://conda.anaconda.org/conda-forge/noarch/userpath-1.9.2-pyhd8ed1ab_0.conda
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-  - python >=3.9
-  license: MIT
-  license_family: MIT
-  purls:
-  - pkg:pypi/userpath?source=hash-mapping
-  size: 14292
-  timestamp: 1735925027874
-- conda: https://conda.anaconda.org/conda-forge/linux-64/uv-0.7.16-h29fcd0c_1.conda
-  sha256: fc41b5c92c4080ba4594d594463ef80c0f6041cf2b0ffcebc17d731a693bb811
-  md5: fc9c15e81c00d992c501aec4cbf097a5
-  depends:
-  - __glibc >=2.17,<3.0.a0
-  - libstdcxx >=13
-  - libgcc >=13
-  constrains:
-  - __glibc >=2.17
-  license: Apache-2.0 OR MIT
-  purls: []
-  size: 14265772
-  timestamp: 1751302016738
 - conda: https://conda.anaconda.org/conda-forge/noarch/versioningit-3.3.0-pyhd8ed1ab_0.conda
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   md5: 57b96d99ac0f5a548f7001618db6a561
@@ -6092,6 +5638,17 @@ packages:
   - pkg:pypi/wheel?source=hash-mapping
   size: 62931
   timestamp: 1733130309598
+- conda: https://conda.anaconda.org/conda-forge/noarch/wheel-filename-1.4.2-pyhd8ed1ab_0.conda
+  sha256: 00687e1e0449e764543f8bac28c81ae40ca1f0b0fce9ab80faf3a5a361ac7012
+  md5: 51fa875ce75cbd653e0145830e3c6035
+  depends:
+  - python >=3.9
+  license: MIT
+  license_family: MIT
+  purls:
+  - pkg:pypi/wheel-filename?source=hash-mapping
+  size: 11507
+  timestamp: 1733242371484
 - conda: https://conda.anaconda.org/conda-forge/linux-64/xcb-util-0.4.1-h4f16b4b_2.conda
   sha256: ad8cab7e07e2af268449c2ce855cbb51f43f4664936eff679b1f3862e6e4b01d
   md5: fdc27cb255a7a2cc73b7919a968b48f0
diff --git a/pyproject.toml b/pyproject.toml
index 5cacbe75..3aa43702 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,8 +21,6 @@ shiver = "shiver.shiver:gui"
 [build-system]
 requires = [
   "hatchling",
-  "wheel",
-  "toml",
   "versioningit"
 ]
 build-backend = "hatchling.build"
@@ -96,7 +94,6 @@ versioningit = "*"
 
 [tool.pixi.package.run-dependencies]
 #dependencies for the conda package - for shiver to run
-toml = ">=0.10.2,<0.11"
 mantidworkbench = ">=6.12"
 pyoncat = ">=2.1"
 pyoncatqt =">=1.2.0"
@@ -104,7 +101,6 @@ configupdater = "*"
 
 [tool.pixi.dependencies]
 # Conda package dependencies for the local environment though pixi
-toml = ">=0.10.2,<0.11"
 mantidworkbench = ">=6.12"
 pyoncat = ">=2.1"
 pyoncatqt =">=1.2.0"
@@ -114,7 +110,6 @@ configupdater = "*"
 # PyPI dependencies for the local environment though pixi
 #including this package to allow local editable installs
 shiver = { path = ".", editable = true }
-toml-cli = ">=0.7.0,<0.8"
 
 [tool.pixi.environments]
 #environment definitions with feature dependencies
@@ -122,17 +117,20 @@ default = { features = ["package", "developer","docs","test",], solve-group = "d
 
 [tool.pixi.feature.package.dependencies]
 #conda package
-anaconda-client = ">=1.13.0,<2"
-twine = ">=6.1.0,<7"
-versioningit = "*"
-hatch = "*"
+anaconda-client = ">=1.13.0"
+check-wheel-contents = ">=0.6.2"
+versioningit = ">=3.2.0"
 #python package
 pip = "*"
 
+[tool.pixi.feature.package.pypi-dependencies]
+toml-cli = "*"
+
 #code analysis tools
 [tool.pixi.feature.developer.dependencies]
-pip-audit = ">=2.9.0,<3"
-pre-commit = "*"
+pip = ">=25.1.1"
+pip-audit = ">=2.9.0"
+pre-commit = ">=4.2.0"
 pylint = "*"
 codecov = ">=2.1.13"
 
@@ -150,27 +148,30 @@ pytest-mock = ">=3.14.1"
 pytest-xvfb = ">=3.1.1"
 
 [tool.pixi.tasks]
-# PyPI
-build-sdist = { cmd = "hatch build sdist", description = "Build the source distribution (tar.gz)" }
-build-pypi = { cmd = "hatch build", description = "Build the package for PyPI" }
-clean-pypi = { cmd = "rm -rf dist", description = "Clean the PyPI build artifacts" }
-publish-pypi = { cmd = "twine upload dist/*", description = "Publish the package to PyPI", depends-on = [
-  "build-pypi",
+# Documentation
+build-docs = { cmd = 'sphinx-build -b html docs/source/ docs/_build/html', description = "Build documentation" }
+test-docs = { cmd = "sphinx-build -M doctest docs/source/ docs/_build/html", description = "Test building the documentation" }
+# Testing
+test = { description = "Run the test suite", cmd = "pytest" }
+# Packaging
+conda-build-command = { cmd = "pixi build", description = "Wrapper for building the conda package - used by `conda-build`" }
+conda-build = { description = "Build the conda package", depends-on = [
+    "sync-version",
+    "conda-build-command",
+    "reset-version",
 ] }
-# Conda
-build-conda-command = { cmd = "pixi build", description = "Build the conda package command" }
-build-conda = { description = "Build the conda package", depends-on = [
-  "sync-version",
-  "build-conda-command",
-  "reset-version",
+conda-publish = { cmd = "anaconda upload *.conda", description = "Publish the .conda package to anaconda.org", depends-on = [
+    "conda-build",
 ] }
-clean-conda = { cmd = "rm shiver-*.conda", description = "Clean the conda build artifacts" }
-# MISC
-clean-all = { description = "Clean all build artifacts", depends-on = [
-  "reset-version",
-  "clean-pypi",
-  "clean-conda",
+# Misc
+audit-deps = { cmd = "pip-audit --local -s osv", description = "Audit the package dependencies for vulnerabilities" }
+clean = { cmd = 'rm -rf .pytest_cache .ruff_cache **/*.egg-info **/dist **/__pycache__ **/_version.py', description = "Clean up various caches and build artifacts" }
+clean-conda = { cmd = "rm -f *.conda", description = "Clean the local .conda build artifacts" }
+clean-docs = { cmd = "rm -rf docs/_build", description = "Clean up documentation build artifacts" }
+clean-all = { description = "Clean all artifacts", depends-on = [
+    "clean",
+    "clean-conda",
+    "clean-docs",
 ] }
-sync-version = { cmd = "version=$(python -m versioningit); toml set tool.pixi.package.version \"$version\" --toml-path pyproject.toml" }
+sync-version = { cmd = 'version=$(python -m versioningit); toml set tool.pixi.package.version "$version" --toml-path pyproject.toml', description = "Sync pyproject.toml version with Git version" }
 reset-version = { cmd = "toml set tool.pixi.package.version \"0.0.0\" --toml-path pyproject.toml", description = "Reset the package version to 0.0.0" }
-audit-deps = { cmd = "pip-audit --local -s osv" }

From be52812a18b7cb9014b7974ed987cc6ea59a2af8 Mon Sep 17 00:00:00 2001
From: "Patrou, Maria" <patroum@ornl.gov>
Date: Thu, 3 Jul 2025 13:47:35 -0400
Subject: [PATCH 53/53] typo

---
 docs/source/getting_started.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst
index 79b64c1a..8832d207 100644
--- a/docs/source/getting_started.rst
+++ b/docs/source/getting_started.rst
@@ -51,7 +51,7 @@ Any change to pyproject.toml, e.g. new dependencies, requires updating the pixi.
 
 .. code-block:: bash
 
-    pixi.lock
+    pixi lock
 
 To run all tests for ``SHIVER``