Pin libsqlite=3.50.4 to workaround undefined symbol: sqlite3_total_changes64 error (#63)

* Activate try-gmt environment in setup-miniconda step

* Bump jupyterlab to 4.5.1, jupyter-offlinenotebook to 0.3.2, geopandas to 1.1.2

* Set use-mamba: true instead of conda-solver: libmamba

* install repo2docker into test environment only

No need to install from environment.yml twice, since repo2docker does a separate clean install.

* Install repo2docker using pip

instead of conda/mamba. Should pull in jupyter-repo2docker 2025.12.0 instead of 2025.8.0

* Pin jupyterlab to 4.4.9

Match version at https://github.com/jupyterhub/repo2docker/blob/2025.12.0/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock#L175

* Pin libsqlite to 3.50.4

Match https://github.com/jupyterhub/repo2docker/blob/2025.12.0/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock#L31, try to prevent other versions of sqlite/libsqlite from being pulled in.

Author: weiji14

.github/workflows/repo2docker.yml

@@ -9,26 +9,21 @@ jobs:
   repo2docker:
     name: Run repo2docker
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
       - name: Checkout
         uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
-
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@835234971496cad1653abb28a638a281cf32541f # v3.2.0
         with:
-          conda-remove-defaults: "true"
-          conda-solver: libmamba
-          miniforge-version: latest
-
-      - name: Install dependencies
-        shell: bash -l {0}
-        run: conda install jupyter-repo2docker
+          persist-credentials: false
 
-      - name: Show installed package
-        shell: bash -l {0}
-        run: conda list
+      - name: Set up Python and install repo2docker
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
+        with:
+          python-version: "3.13"
+          pip-install: jupyter-repo2docker
 
       - name: Run repo2docker
-        shell: bash -l {0}
         run: jupyter-repo2docker --no-run --ref ${{ github.event.pull_request.head.sha }} https://github.com/${{ github.event.pull_request.head.repo.full_name }}

environment.yml

@@ -6,7 +6,10 @@ dependencies:
   - python=3.13
   - gmt=6.6.0
   - pygmt=0.17.0
-  - jupyterlab=4.3.6
-  - jupyter-offlinenotebook=0.3.1
+  - jupyterlab=4.4.9
+  - jupyter-offlinenotebook=0.3.2
   # Optional dependencies
-  - geopandas=1.1.1
+  - geopandas=1.1.2
+  # Temporary pin libsqlite to workaround `undefined symbol: sqlite3_total_changes64`
+  # https://github.com/GenericMappingTools/try-gmt/pull/63
+  - libsqlite=3.50.4