From 8d5475cfbc33603d5410bb06febb7004b9735cd9 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 5 Jan 2026 11:08:27 +1300 Subject: [PATCH 1/7] Activate try-gmt environment in setup-miniconda step --- .github/workflows/repo2docker.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/repo2docker.yml b/.github/workflows/repo2docker.yml index 3040159..6323493 100644 --- a/.github/workflows/repo2docker.yml +++ b/.github/workflows/repo2docker.yml @@ -17,8 +17,10 @@ jobs: - name: Setup Miniconda uses: conda-incubator/setup-miniconda@835234971496cad1653abb28a638a281cf32541f # v3.2.0 with: + activate-environment: try-gmt conda-remove-defaults: "true" conda-solver: libmamba + environment-file: environment.yml miniforge-version: latest - name: Install dependencies From f559aab7e04823fb984204a0c514c45c25c0c7dd Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 5 Jan 2026 11:51:48 +1300 Subject: [PATCH 2/7] Bump jupyterlab to 4.5.1, jupyter-offlinenotebook to 0.3.2, geopandas to 1.1.2 --- environment.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index 40812f5..9f661aa 100644 --- a/environment.yml +++ b/environment.yml @@ -6,7 +6,7 @@ dependencies: - python=3.13 - gmt=6.6.0 - pygmt=0.17.0 - - jupyterlab=4.3.6 - - jupyter-offlinenotebook=0.3.1 + - jupyterlab=4.5.1 + - jupyter-offlinenotebook=0.3.2 # Optional dependencies - - geopandas=1.1.1 + - geopandas=1.1.2 From 962c629a12ccb11fe291ffbbbf46e90124021e54 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 5 Jan 2026 12:11:28 +1300 Subject: [PATCH 3/7] Set use-mamba: true instead of conda-solver: libmamba --- .github/workflows/repo2docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/repo2docker.yml b/.github/workflows/repo2docker.yml index 6323493..2772ad6 100644 --- a/.github/workflows/repo2docker.yml +++ b/.github/workflows/repo2docker.yml @@ -19,9 +19,9 @@ jobs: with: activate-environment: try-gmt conda-remove-defaults: "true" - conda-solver: libmamba environment-file: environment.yml miniforge-version: latest + use-mamba: true - name: Install dependencies shell: bash -l {0} From 0cd91944a59886b53c1dea50bf12bc23a46092c0 Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 5 Jan 2026 15:39:30 +1300 Subject: [PATCH 4/7] install repo2docker into test environment only No need to install from environment.yml twice, since repo2docker does a separate clean install. --- .github/workflows/repo2docker.yml | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/.github/workflows/repo2docker.yml b/.github/workflows/repo2docker.yml index 2772ad6..e132d3d 100644 --- a/.github/workflows/repo2docker.yml +++ b/.github/workflows/repo2docker.yml @@ -9,6 +9,9 @@ jobs: repo2docker: name: Run repo2docker runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} steps: - name: Checkout @@ -17,20 +20,15 @@ jobs: - name: Setup Miniconda uses: conda-incubator/setup-miniconda@835234971496cad1653abb28a638a281cf32541f # v3.2.0 with: - activate-environment: try-gmt conda-remove-defaults: "true" - environment-file: environment.yml miniforge-version: latest use-mamba: true - - name: Install dependencies - shell: bash -l {0} - run: conda install jupyter-repo2docker + - name: Install repo2docker + run: mamba install jupyter-repo2docker - - name: Show installed package - shell: bash -l {0} - run: conda list + - name: Show installed packages + run: mamba list - 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 }} From 4153739304c66688570b8963b4531b74ad61a33b Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 5 Jan 2026 16:29:48 +1300 Subject: [PATCH 5/7] Install repo2docker using pip instead of conda/mamba. Should pull in jupyter-repo2docker 2025.12.0 instead of 2025.8.0 --- .github/workflows/repo2docker.yml | 17 ++++++----------- 1 file changed, 6 insertions(+), 11 deletions(-) diff --git a/.github/workflows/repo2docker.yml b/.github/workflows/repo2docker.yml index e132d3d..f1a1b2c 100644 --- a/.github/workflows/repo2docker.yml +++ b/.github/workflows/repo2docker.yml @@ -16,19 +16,14 @@ jobs: 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" - miniforge-version: latest - use-mamba: true - - - name: Install repo2docker - run: mamba install jupyter-repo2docker + persist-credentials: false - - name: Show installed packages - run: mamba 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 run: jupyter-repo2docker --no-run --ref ${{ github.event.pull_request.head.sha }} https://github.com/${{ github.event.pull_request.head.repo.full_name }} From 3526fc13ad9e8c1a6368e628316fd4b01d5f3cbc Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 5 Jan 2026 16:44:22 +1300 Subject: [PATCH 6/7] 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 --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 9f661aa..ad840ba 100644 --- a/environment.yml +++ b/environment.yml @@ -6,7 +6,7 @@ dependencies: - python=3.13 - gmt=6.6.0 - pygmt=0.17.0 - - jupyterlab=4.5.1 + - jupyterlab=4.4.9 - jupyter-offlinenotebook=0.3.2 # Optional dependencies - geopandas=1.1.2 From 0468aa4f8801a6bbaf05ae3ccf4dd86e442c388f Mon Sep 17 00:00:00 2001 From: Wei Ji <23487320+weiji14@users.noreply.github.com> Date: Mon, 5 Jan 2026 17:12:37 +1300 Subject: [PATCH 7/7] 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. --- environment.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/environment.yml b/environment.yml index ad840ba..c6dd6c6 100644 --- a/environment.yml +++ b/environment.yml @@ -10,3 +10,6 @@ dependencies: - jupyter-offlinenotebook=0.3.2 # Optional dependencies - 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