From 1b0caf7adba0f9f9b72b2ef9fa04b4fd0f4fb5b3 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 22:33:43 +0100 Subject: [PATCH 01/20] start debugging --- .github/workflows/gh-ci-cron.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 93f3d279..f671728b 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -20,16 +20,16 @@ defaults: jobs: gen_matrix: - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest outputs: matrix: ${{ steps.get-mdakits.outputs.matrix }} steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - id: get-python - uses: actions/setup-python@v4 + uses: actions/setup-python@v6 with: - python-version: "3.12" + python-version: "3.13" - id: get-mdakits run: | @@ -43,9 +43,9 @@ jobs: python-min: ${{ steps.get-compatible-python.outputs.oldest-python }} steps: - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v6 with: - python-version: "3.12" + python-version: "3.13" - id: get-compatible-python uses: MDAnalysis/mdanalysis-compatible-python@main From 823eaa58374bb0d1264a4dfa45036ffc59f8a5da Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 22:49:01 +0100 Subject: [PATCH 02/20] try fixing a few more things for now --- .github/workflows/gh-ci-cron.yaml | 26 +++++++++++++------------- .github/workflows/gh-ci.yaml | 20 ++++++++++---------- 2 files changed, 23 insertions(+), 23 deletions(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index f671728b..68948508 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -54,14 +54,14 @@ jobs: mdakit-ci: needs: [gen_matrix, env_config] - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest strategy: fail-fast: false matrix: mdakit: ${{fromJSON(needs.gen_matrix.outputs.matrix)}} jobstep: ['latest', 'develop'] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - id: get-base-python-deps name: get-base-python-deps @@ -79,7 +79,7 @@ jobs: - id: install-conda-env name: install-conda-env - uses: conda-incubator/setup-miniconda@v3 + uses: conda-incubator/setup-miniconda@v4 with: python-version: ${{ env.PYVER }} add-pip-as-python-dependency: true @@ -153,7 +153,7 @@ jobs: - id: upload-artifacts name: upload-artifacts - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: cron-statuses-${{ matrix.mdakit }}-${{ matrix.jobstep }} path: ${{ matrix.mdakit }}-${{ matrix.jobstep }}-statuses.json @@ -163,16 +163,16 @@ jobs: process_results: if: ${{ always() }} needs: mdakit-ci - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest permissions: contents: write pull-requests: write packages: none issues: write steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - - uses: actions/download-artifact@v4 + - uses: actions/download-artifact@v8 with: path: json-statuses/ @@ -191,7 +191,7 @@ jobs: env: GITHUB_TOKEN: ${{ github.token }} - - uses: stefanzweifel/git-auto-commit-action@v4 + - uses: stefanzweifel/git-auto-commit-action@v7 with: commit_message: commit changes to status files skip_dirty_check: false @@ -200,22 +200,22 @@ jobs: deploy_docs: if: ${{ always() }} needs: process_results - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: setup_micromamba - uses: mamba-org/setup-micromamba@v1 + uses: mamba-org/setup-micromamba@v3 with: environment-file: docs/requirements.yaml environment-name: MDAKitRegistry-docs create-args: >- - python=3.9 + python=3.12 pip - name: build_docs run: | cd docs && sphinx-build -b html source build - name: deploy docs - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./docs/build diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index e7a92342..e998c39d 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -16,20 +16,20 @@ defaults: jobs: gen_matrix: - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest outputs: matrix: ${{ steps.get-changed-mdakits.outputs.matrix }} steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - id: get-python - uses: actions/setup-python@v4 + uses: actions/setup-python@v6 with: - python-version: 3.9 + python-version: 3.13 - id: files name: get changed filed - uses: masesgroup/retrieve-changed-files@v3 + uses: masesgroup/retrieve-changed-files@v4 with: format: 'json' - id: get-changed-mdakits @@ -46,9 +46,9 @@ jobs: python-stable: ${{ steps.get-compatible-python.outputs.stable-python }} python-min: ${{ steps.get-compatible-python.outputs.oldest-python }} steps: - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v6 with: - python-version: "3.12" + python-version: "3.13" - id: get-compatible-python uses: MDAnalysis/mdanalysis-compatible-python@main @@ -57,14 +57,14 @@ jobs: mdakit-ci: needs: [gen_matrix, env_config] - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest strategy: fail-fast: false matrix: mdakit: ${{fromJSON(needs.gen_matrix.outputs.matrix)}} jobstep: ['latest', 'develop'] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - id: get-base-python-deps name: get-base-python-deps @@ -82,7 +82,7 @@ jobs: - id: install-conda-env name: install-conda-env - uses: conda-incubator/setup-miniconda@v3 + uses: conda-incubator/setup-miniconda@v4 with: python-version: ${{ env.PYVER }} add-pip-as-python-dependency: true From 6393f44c9646dae1a2baa5d0c95677145af2b9ef Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 22:51:30 +0100 Subject: [PATCH 03/20] Slightly modify propkatraj yaml for testing --- mdakits/propkatraj/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index 1c9e44d8..9886e6d0 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -15,7 +15,7 @@ project_home: https://github.com/Becksteinlab/propkatraj/ documentation_home: https://becksteinlab.github.io/propkatraj/ documentation_type: UserGuide + API -## Optional entries +## Some optional entries install: - pip install propkatraj src_install: From d22df3c1d9a28d4774fa376c5bd030bdaef786ae Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 22:56:33 +0100 Subject: [PATCH 04/20] maybe a missing channel? --- mdakits/propkatraj/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index 9886e6d0..15a04741 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -25,7 +25,7 @@ mdanalysis_requires: ">=2.0.0" run_tests: - pytest --pyargs propkatraj.tests test_dependencies: - - mamba install pytest MDAnalysisTests + - mamba install -c conda-forge pytest MDAnalysisTests project_org: Becksteinlab development_status: Mature publications: From f7fe10a1a9757d40d1bd6ccfb798f246f6cff378 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 22:59:31 +0100 Subject: [PATCH 05/20] list env info before failing step --- .github/workflows/gh-ci.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index e998c39d..00bb3208 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -114,6 +114,12 @@ jobs: echo "install=${install}" eval ${install} + - id: debug-env + name: debug-env + run: | + mamba list + pip list + - id: install-test-deps name: install-test-deps continue-on-error: false From 9c05f3df284f40273196dae4a9cf4c3ed669397c Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 23:04:00 +0100 Subject: [PATCH 06/20] prepend with python -m --- .github/workflows/gh-ci.yaml | 6 +++--- mdakits/propkatraj/metadata.yaml | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 00bb3208..fb8907ba 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -69,7 +69,7 @@ jobs: - id: get-base-python-deps name: get-base-python-deps run: | - pip install requests setuptools packaging pyyaml pydantic PyGithub + python -m pip install requests setuptools packaging pyyaml pydantic PyGithub - id: check-set-python-bounds name: check-set-python-bounds @@ -98,7 +98,7 @@ jobs: name: install-conda-base-deps run: | mamba install requests setuptools packaging pyyaml pydantic - pip install PyGithub + python -m pip install PyGithub - id: install-mdakit name: install-mdakit @@ -118,7 +118,7 @@ jobs: name: debug-env run: | mamba list - pip list + python -m pip list - id: install-test-deps name: install-test-deps diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index 15a04741..49891a05 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -17,9 +17,9 @@ documentation_type: UserGuide + API ## Some optional entries install: - - pip install propkatraj + - python -m pip install propkatraj src_install: - - pip install git+https://github.com/Becksteinlab/propkatraj@main + - python -m pip install git+https://github.com/Becksteinlab/propkatraj@main python_requires: ">=3.8" mdanalysis_requires: ">=2.0.0" run_tests: From a170f87ee0d36257d2e02b61b2928b2f47cc8a02 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 23:07:23 +0100 Subject: [PATCH 07/20] try removing a couple of things --- .github/workflows/gh-ci.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index fb8907ba..6c3311f7 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -86,11 +86,9 @@ jobs: with: python-version: ${{ env.PYVER }} add-pip-as-python-dependency: true - architecture: x64 use-mamba: true miniforge-version: latest channels: conda-forge - channel-priority: flexible auto-update-conda: true show-channel-urls: true From 2cd7086c354a5df3e98721df8c6741c7789ad6f5 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 23:14:01 +0100 Subject: [PATCH 08/20] debug manual forcing --- .github/workflows/gh-ci.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 6c3311f7..d65fdb1b 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -118,6 +118,10 @@ jobs: mamba list python -m pip list + - id: debug-mdanalysistests + run: | + mamba install -vv -c conda-forge mdanalysistests + - id: install-test-deps name: install-test-deps continue-on-error: false From 64d925e79fb83991bbd6301201adc7382f5fdf79 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 23:21:44 +0100 Subject: [PATCH 09/20] try guarding the eval --- .github/workflows/gh-ci.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index d65fdb1b..93aebe10 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -118,9 +118,9 @@ jobs: mamba list python -m pip list - - id: debug-mdanalysistests - run: | - mamba install -vv -c conda-forge mdanalysistests + #- id: debug-mdanalysistests + # run: | + # mamba install -c conda-forge mdanalysistests - id: install-test-deps name: install-test-deps @@ -128,7 +128,7 @@ jobs: run: | install=$(python utils/get_testdeps.py --mdakit ${{matrix.mdakit}}) echo "install tests:${install}" - eval ${install} + eval "${install}" - id: install-mdanalysis name: install-mdanalysis From 0c4c353242807175102a6f95609a232f6a5ca05b Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 23:22:08 +0100 Subject: [PATCH 10/20] add some verbosity too --- mdakits/propkatraj/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index 49891a05..25de49e4 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -25,7 +25,7 @@ mdanalysis_requires: ">=2.0.0" run_tests: - pytest --pyargs propkatraj.tests test_dependencies: - - mamba install -c conda-forge pytest MDAnalysisTests + - mamba install -v -c conda-forge pytest MDAnalysisTests project_org: Becksteinlab development_status: Mature publications: From c58bb4aadb55ea953f7aa31627097685ce17407c Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 23:24:22 +0100 Subject: [PATCH 11/20] try adding a spare space at the end --- mdakits/propkatraj/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index 25de49e4..eed76bb3 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -25,7 +25,7 @@ mdanalysis_requires: ">=2.0.0" run_tests: - pytest --pyargs propkatraj.tests test_dependencies: - - mamba install -v -c conda-forge pytest MDAnalysisTests + - mamba install -v -c conda-forge pytest MDAnalysisTests project_org: Becksteinlab development_status: Mature publications: From 3fb5a79c0d1ccb680463d6a0b9791113edce51f8 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 23:26:26 +0100 Subject: [PATCH 12/20] what if I add a version pin? --- mdakits/propkatraj/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index eed76bb3..c7d5f5cf 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -25,7 +25,7 @@ mdanalysis_requires: ">=2.0.0" run_tests: - pytest --pyargs propkatraj.tests test_dependencies: - - mamba install -v -c conda-forge pytest MDAnalysisTests + - mamba install -v -c conda-forge pytest "MDAnalysisTests>=2.0" project_org: Becksteinlab development_status: Mature publications: From 134e5f88ff00550fa3d22ec6f33ccbbcce059270 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 23:33:19 +0100 Subject: [PATCH 13/20] will it complain if there's something else at the end? --- .github/workflows/gh-ci.yaml | 2 +- mdakits/propkatraj/metadata.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 93aebe10..40424ffb 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -128,7 +128,7 @@ jobs: run: | install=$(python utils/get_testdeps.py --mdakit ${{matrix.mdakit}}) echo "install tests:${install}" - eval "${install}" + eval "${install} -v" - id: install-mdanalysis name: install-mdanalysis diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index c7d5f5cf..49891a05 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -25,7 +25,7 @@ mdanalysis_requires: ">=2.0.0" run_tests: - pytest --pyargs propkatraj.tests test_dependencies: - - mamba install -v -c conda-forge pytest "MDAnalysisTests>=2.0" + - mamba install -c conda-forge pytest MDAnalysisTests project_org: Becksteinlab development_status: Mature publications: From 328d974f365f394abd9b2fc5812d1dd8a063f973 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 23:42:26 +0100 Subject: [PATCH 14/20] is this a problem with eval? --- .github/workflows/gh-ci.yaml | 6 ++++-- mdakits/propkatraj/metadata.yaml | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 40424ffb..aedd8ab5 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -127,8 +127,10 @@ jobs: continue-on-error: false run: | install=$(python utils/get_testdeps.py --mdakit ${{matrix.mdakit}}) - echo "install tests:${install}" - eval "${install} -v" + echo "test installs: ${install}" + read -ra cmd <<< "$install" + "${cmd[@]}" + #eval "${install}" - id: install-mdanalysis name: install-mdanalysis diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index 49891a05..25de49e4 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -25,7 +25,7 @@ mdanalysis_requires: ">=2.0.0" run_tests: - pytest --pyargs propkatraj.tests test_dependencies: - - mamba install -c conda-forge pytest MDAnalysisTests + - mamba install -v -c conda-forge pytest MDAnalysisTests project_org: Becksteinlab development_status: Mature publications: From f17b669e82380b503b31a39ff5c2eb7768ee8fb7 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Sun, 31 May 2026 23:45:01 +0100 Subject: [PATCH 15/20] maybe it's capitalization? --- .github/workflows/gh-ci.yaml | 4 +--- mdakits/propkatraj/metadata.yaml | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index aedd8ab5..19739ceb 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -128,9 +128,7 @@ jobs: run: | install=$(python utils/get_testdeps.py --mdakit ${{matrix.mdakit}}) echo "test installs: ${install}" - read -ra cmd <<< "$install" - "${cmd[@]}" - #eval "${install}" + eval "${install}" - id: install-mdanalysis name: install-mdanalysis diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index 25de49e4..b33aea6e 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -25,7 +25,7 @@ mdanalysis_requires: ">=2.0.0" run_tests: - pytest --pyargs propkatraj.tests test_dependencies: - - mamba install -v -c conda-forge pytest MDAnalysisTests + - mamba install -v -c conda-forge pytest mdanalysistests project_org: Becksteinlab development_status: Mature publications: From 96dc694774744449b93e8b820dba79e72d813ef1 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 1 Jun 2026 00:24:23 +0100 Subject: [PATCH 16/20] lowercase on install instructions --- utils/get_install.py | 2 +- utils/get_testdeps.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/utils/get_install.py b/utils/get_install.py index 6f4b3983..bead02d7 100644 --- a/utils/get_install.py +++ b/utils/get_install.py @@ -53,4 +53,4 @@ args = parser.parse_args() kit = MDAKit(f"mdakits/{args.mdakit}") instructions = kit.get_install(f"{args.itype}") - print(instructions) + print(instructions.lower()) diff --git a/utils/get_testdeps.py b/utils/get_testdeps.py index bd878075..1558b7b3 100644 --- a/utils/get_testdeps.py +++ b/utils/get_testdeps.py @@ -46,4 +46,4 @@ args = parser.parse_args() kit = MDAKit(f"mdakits/{args.mdakit}") instructions = kit.get_test_deps() - print(instructions) + print(instructions.lower()) From 27637aa33bcdaf4c1436e6b548c489108996da9b Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 1 Jun 2026 00:26:47 +0100 Subject: [PATCH 17/20] some fixes --- .github/workflows/gh-ci-cron.yaml | 1 - .github/workflows/gh-ci.yaml | 11 +---------- mdakits/propkatraj/metadata.yaml | 6 +++--- 3 files changed, 4 insertions(+), 14 deletions(-) diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml index 68948508..aae66c1d 100644 --- a/.github/workflows/gh-ci-cron.yaml +++ b/.github/workflows/gh-ci-cron.yaml @@ -83,7 +83,6 @@ jobs: with: python-version: ${{ env.PYVER }} add-pip-as-python-dependency: true - architecture: x64 use-mamba: true miniforge-version: latest channels: conda-forge diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 19739ceb..439a2441 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -89,6 +89,7 @@ jobs: use-mamba: true miniforge-version: latest channels: conda-forge + channel-priority: flexible auto-update-conda: true show-channel-urls: true @@ -112,16 +113,6 @@ jobs: echo "install=${install}" eval ${install} - - id: debug-env - name: debug-env - run: | - mamba list - python -m pip list - - #- id: debug-mdanalysistests - # run: | - # mamba install -c conda-forge mdanalysistests - - id: install-test-deps name: install-test-deps continue-on-error: false diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index b33aea6e..9886e6d0 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -17,15 +17,15 @@ documentation_type: UserGuide + API ## Some optional entries install: - - python -m pip install propkatraj + - pip install propkatraj src_install: - - python -m pip install git+https://github.com/Becksteinlab/propkatraj@main + - pip install git+https://github.com/Becksteinlab/propkatraj@main python_requires: ">=3.8" mdanalysis_requires: ">=2.0.0" run_tests: - pytest --pyargs propkatraj.tests test_dependencies: - - mamba install -v -c conda-forge pytest mdanalysistests + - mamba install pytest MDAnalysisTests project_org: Becksteinlab development_status: Mature publications: From 660ed839f2ee62713029778af41ff9d60bf55c64 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 1 Jun 2026 00:31:36 +0100 Subject: [PATCH 18/20] see if this will work --- mdakits/mdachecker/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/mdachecker/metadata.yaml b/mdakits/mdachecker/metadata.yaml index 2cd115a9..3273c10d 100644 --- a/mdakits/mdachecker/metadata.yaml +++ b/mdakits/mdachecker/metadata.yaml @@ -15,7 +15,7 @@ project_home: https://github.com/IAlibay/CheckStructure/ documentation_home: https://github.com/IAlibay/CheckStructure/blob/main/README.md documentation_type: README -## Optional entries +## Some optional entries install: - pip install git+https://github.com/IAlibay/CheckStructure@main src_install: From 3656535936f50514099e067d5ca34c110e16607a Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 1 Jun 2026 00:35:49 +0100 Subject: [PATCH 19/20] see if it'll fix mdacli --- mdakits/mdacli/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mdakits/mdacli/metadata.yaml b/mdakits/mdacli/metadata.yaml index db2ccf3c..922789ef 100644 --- a/mdakits/mdacli/metadata.yaml +++ b/mdakits/mdacli/metadata.yaml @@ -15,7 +15,7 @@ project_home: https://github.com/MDAnalysis/mdacli documentation_home: https://mdacli.readthedocs.io/ documentation_type: UserGuide + API -## Optional entries +## Some Optional entries install: - mamba install -c conda-forge mdacli src_install: From 7539358a4525a0febb96862da37a082ad9084259 Mon Sep 17 00:00:00 2001 From: IAlibay Date: Mon, 1 Jun 2026 00:39:15 +0100 Subject: [PATCH 20/20] Revert yaml changes --- mdakits/mdachecker/metadata.yaml | 2 +- mdakits/mdacli/metadata.yaml | 2 +- mdakits/propkatraj/metadata.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/mdakits/mdachecker/metadata.yaml b/mdakits/mdachecker/metadata.yaml index 3273c10d..2cd115a9 100644 --- a/mdakits/mdachecker/metadata.yaml +++ b/mdakits/mdachecker/metadata.yaml @@ -15,7 +15,7 @@ project_home: https://github.com/IAlibay/CheckStructure/ documentation_home: https://github.com/IAlibay/CheckStructure/blob/main/README.md documentation_type: README -## Some optional entries +## Optional entries install: - pip install git+https://github.com/IAlibay/CheckStructure@main src_install: diff --git a/mdakits/mdacli/metadata.yaml b/mdakits/mdacli/metadata.yaml index 922789ef..db2ccf3c 100644 --- a/mdakits/mdacli/metadata.yaml +++ b/mdakits/mdacli/metadata.yaml @@ -15,7 +15,7 @@ project_home: https://github.com/MDAnalysis/mdacli documentation_home: https://mdacli.readthedocs.io/ documentation_type: UserGuide + API -## Some Optional entries +## Optional entries install: - mamba install -c conda-forge mdacli src_install: diff --git a/mdakits/propkatraj/metadata.yaml b/mdakits/propkatraj/metadata.yaml index 9886e6d0..1c9e44d8 100644 --- a/mdakits/propkatraj/metadata.yaml +++ b/mdakits/propkatraj/metadata.yaml @@ -15,7 +15,7 @@ project_home: https://github.com/Becksteinlab/propkatraj/ documentation_home: https://becksteinlab.github.io/propkatraj/ documentation_type: UserGuide + API -## Some optional entries +## Optional entries install: - pip install propkatraj src_install: