From 2d6d8a1f9f901bc6cdd4dba6ab9ae4e8eac02d43 Mon Sep 17 00:00:00 2001 From: Craig Russell Date: Thu, 16 Nov 2023 16:54:44 +0000 Subject: [PATCH 1/7] adding poetry support --- pyproject.toml | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 4e42573ba..f0947af35 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,34 @@ +[tool.poetry] +name = "biospec" +version = "0.1.0" +description = "" +authors = ["Your Name "] + +[tool.poetry.dependencies] +python = "^3.8" +numpy = "*" +pydantic = {version = ">=2.0.1"} +packaging = {version = ">=17.0"} +ruamel-yaml = "^0.18.5" +deepdiff = "^6.7.1" +email-validator = "^2.1.0.post1" +python-dateutil = "^2.8.2" +annotated-types = "^0.6.0" +typing-extensions = "^4.8.0" +lxml = "^4.9.3" + +[tool.poetry.group.dev.dependencies] +pytest-cov = "^4.1.0" +black = "^23.11.0" +pyright = "^1.1.336" +pooch = "^1.8.0" +pre-commit = "^3.5.0" +pytest = "^7.4.3" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" + [tool.black] line-length = 120 target-version = ['py38'] From c9ee9759bb8ccc627927bde7be9dfbc806adabef Mon Sep 17 00:00:00 2001 From: Craig Russell Date: Thu, 16 Nov 2023 16:57:22 +0000 Subject: [PATCH 2/7] checking it installs --- pyproject.toml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f0947af35..780121a81 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,10 @@ [tool.poetry] -name = "biospec" -version = "0.1.0" +name = "bioimageio-spec" +version = "0.5.0" description = "" -authors = ["Your Name "] +authors = ["Bioimage.IO Contributors"] +packages = [{include = "spec", from="bioimageio"}] + [tool.poetry.dependencies] python = "^3.8" From 82638462b876cbdd37267e395c86a42762f68544 Mon Sep 17 00:00:00 2001 From: Craig Russell Date: Thu, 16 Nov 2023 17:03:36 +0000 Subject: [PATCH 3/7] needs pytorch --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 780121a81..990f70846 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,6 +18,7 @@ python-dateutil = "^2.8.2" annotated-types = "^0.6.0" typing-extensions = "^4.8.0" lxml = "^4.9.3" +torch = "^2.1.1" [tool.poetry.group.dev.dependencies] pytest-cov = "^4.1.0" From 5e016d486f767010459c46bc808145fd230fa4c7 Mon Sep 17 00:00:00 2001 From: Craig Russell Date: Thu, 16 Nov 2023 17:20:05 +0000 Subject: [PATCH 4/7] removing python 3.7 test --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 5ab906587..ba762608b 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -26,7 +26,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.7, 3.8, 3.9] + python-version: [3.8, 3.9] steps: - uses: actions/checkout@v3 From b310adef5f3f6baf49c4cdf8c6573eff9ccf77d4 Mon Sep 17 00:00:00 2001 From: Craig Russell Date: Thu, 16 Nov 2023 17:24:34 +0000 Subject: [PATCH 5/7] changing dev group to test for gha --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 990f70846..45e475cfb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ typing-extensions = "^4.8.0" lxml = "^4.9.3" torch = "^2.1.1" -[tool.poetry.group.dev.dependencies] +[tool.poetry.group.test.dependencies] pytest-cov = "^4.1.0" black = "^23.11.0" pyright = "^1.1.336" From cb9badfd68f567bd36f631f883f9bea2383b0fb4 Mon Sep 17 00:00:00 2001 From: Craig Russell Date: Thu, 16 Nov 2023 17:55:25 +0000 Subject: [PATCH 6/7] changing dev group to test for gha v2 --- pyproject.toml | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 45e475cfb..1272485a5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,13 +20,15 @@ typing-extensions = "^4.8.0" lxml = "^4.9.3" torch = "^2.1.1" -[tool.poetry.group.test.dependencies] -pytest-cov = "^4.1.0" -black = "^23.11.0" -pyright = "^1.1.336" -pooch = "^1.8.0" -pre-commit = "^3.5.0" -pytest = "^7.4.3" +pytest-cov = {version="^4.1.0", optional = true} +black = {version="^23.11.0", optional = true} +pyright = {version="^1.1.336", optional = true} +pooch = {version="^1.8.0", optional = true} +pre-commit = {version="^3.5.0", optional = true} +pytest = {version="^7.4.3", optional = true} + +[tool.poetry.extras] +test = ["pytest-cov", "black", "pyright", "pooch", "pre-commit", "pytest"] [build-system] requires = ["poetry-core>=1.0.0"] From a76f277039ea153dd7f36279f11fd725555c390c Mon Sep 17 00:00:00 2001 From: Craig Russell Date: Thu, 16 Nov 2023 18:05:39 +0000 Subject: [PATCH 7/7] fixed cli that I broke --- pyproject.toml | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 1272485a5..b67307ce5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,9 +1,9 @@ [tool.poetry] -name = "bioimageio-spec" +name = "bioimageio" version = "0.5.0" description = "" authors = ["Bioimage.IO Contributors"] -packages = [{include = "spec", from="bioimageio"}] +packages = [{include = "bioimageio" }] [tool.poetry.dependencies] @@ -26,6 +26,9 @@ pyright = {version="^1.1.336", optional = true} pooch = {version="^1.8.0", optional = true} pre-commit = {version="^3.5.0", optional = true} pytest = {version="^7.4.3", optional = true} +marshmallow = "^3.20.1" +marshmallow-union = "^0.1.15.post1" +typer = "^0.9.0" [tool.poetry.extras] test = ["pytest-cov", "black", "pyright", "pooch", "pre-commit", "pytest"] @@ -37,3 +40,7 @@ build-backend = "poetry.core.masonry.api" [tool.black] line-length = 120 target-version = ['py38'] + + +[tool.poetry.scripts] +bioimageio = "bioimageio.spec.__main__:app" \ No newline at end of file