From bb6b2ddd3aa8f156f622fdfe38c12a2133196a59 Mon Sep 17 00:00:00 2001 From: Hugo MacDermott-Opeskin Date: Tue, 16 Jul 2024 11:11:45 +1000 Subject: [PATCH 01/14] Update gh-ci.yaml --- .github/workflows/gh-ci.yaml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index db383e6..2e39f0e 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -12,11 +12,7 @@ on: # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule) - cron: "0 0 * * 0" -concurrency: - # Specific group naming so CI is only cancelled - # within same PR or on merge to main - group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }} - cancel-in-progress: true + defaults: run: From 38ffe256c0e06bfe72ffd418fe1d1f0e8c3d2ceb Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 22 Jul 2024 03:22:01 +0100 Subject: [PATCH 02/14] Update gh-ci.yaml --- .github/workflows/gh-ci.yaml | 44 +++++++++++------------------------- 1 file changed, 13 insertions(+), 31 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 2e39f0e..1128ed9 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -19,30 +19,14 @@ defaults: shell: bash -l {0} jobs: - environment-config: - runs-on: ubuntu-latest - outputs: - stable-python-version: ${{ steps.get-compatible-python.outputs.stable-python }} - python-matrix: ${{ steps.get-compatible-python.outputs.python-versions }} - steps: - - uses: actions/setup-python@v4 - with: - python-version: "3.11" - - - id: get-compatible-python - uses: MDAnalysis/mdanalysis-compatible-python@main - with: - release: "latest" - main-tests: - if: "github.repository == 'lunamorrow/mda_openbabel_converter'" - needs: environment-config + if: "github.repository == 'MDAnalysis/mda-openbabel-converter'" runs-on: ${{ matrix.os }} strategy: fail-fast: false matrix: os: [macOS-latest, ubuntu-latest, windows-latest] - python-version: ${{ fromJSON(needs.environment-config.outputs.python-matrix) }} + python-version: ["3.10", "3.11", "3.12"] mdanalysis-version: ["latest", "develop"] steps: @@ -57,12 +41,11 @@ jobs: # More info on options: https://github.com/conda-incubator/setup-miniconda - name: Install conda dependencies - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: python-version: ${{ matrix.python-version }} environment-file: devtools/conda-envs/test_env.yaml add-pip-as-python-dependency: true - architecture: x64 miniforge-variant: Mambaforge use-mamba: true @@ -99,29 +82,29 @@ jobs: - name: Run tests run: | - pytest -n 2 -v --cov=mda_openbabel_converter --cov-report=xml --color=yes mda_openbabel_converter/tests/ + pytest -n auto -v --cov=mda_openbabel_converter --cov-report=xml --color=yes mda_openbabel_converter/tests/ - name: codecov if: github.repository == 'lunamorrow/mda_openbabel_converter' && github.event_name != 'schedule' - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 with: + token: ${{ secrets.CODECOV_TOKEN }} file: coverage.xml name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} verbose: True pylint_check: - if: "github.repository == 'lunamorrow/mda_openbabel_converter'" - needs: environment-config + if: "github.repository == 'MDAnalysis/mda-openbabel-converter'" runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: - python-version: ${{ needs.environment-config.outputs.stable-python-version }} + python-version: "3.11" - name: Install Pylint run: | @@ -137,17 +120,16 @@ jobs: pypi_check: - if: "github.repository == 'lunamorrow/mda_openbabel_converter'" - needs: environment-config + if: "github.repository == 'MDAnalysis/mda-openbabel-converter'" runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - name: Set up Python ${{ needs.environment-config.outputs.stable-python-version }} - uses: actions/setup-python@v4 + - name: Set up Python + uses: actions/setup-python@v5 with: - python-version: ${{ needs.environment-config.outputs.stable-python-version }} + python-version: "3.11" - name: Install dependencies run: | From 10a35225254d4967d4a057f7433e42b018d91003 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 22 Jul 2024 03:22:01 +0100 Subject: [PATCH 03/14] Update gh-ci.yaml From 177a6d40e0d4af71288136b78004c8c45b4eef5e Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Mon, 22 Jul 2024 03:22:01 +0100 Subject: [PATCH 04/14] Update gh-ci.yaml Merging commits for PR13 and PR14 into PR13. From da98935086509f3e5f565700fec019747a5f75be Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Thu, 18 Jul 2024 14:00:12 +1000 Subject: [PATCH 05/14] Specified less specific openbabel version Adding changes made in PR #12 --- .github/workflows/gh-ci.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 1128ed9..9fbde03 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -68,6 +68,7 @@ jobs: - name: Install package run: | python --version + mamba install -c conda-forge openbabel<3.0.0 python -m pip install . --no-deps - name: Python information From 6d54208e6d4477a52a82ae7cc49f035f24107e72 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Wed, 17 Jul 2024 15:31:18 +1000 Subject: [PATCH 06/14] surely CI works now... more merging... --- mda_openbabel_converter/data/files.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/mda_openbabel_converter/data/files.py b/mda_openbabel_converter/data/files.py index b1f0149..a9518b2 100644 --- a/mda_openbabel_converter/data/files.py +++ b/mda_openbabel_converter/data/files.py @@ -12,6 +12,5 @@ "MDANALYSIS_LOGO", # example file of MDAnalysis logo ] -from pkg_resources import resource_filename - -MDANALYSIS_LOGO = resource_filename(__name__, "mda.txt") +import importlib.resources +MDANALYSIS_LOGO = importlib.resources.files(__name__) / "mda.txt" From 67b510bd701c694d976ced6261a4f168d1fce64d Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Thu, 18 Jul 2024 14:18:04 +1000 Subject: [PATCH 07/14] Fixing new error take 3 and some more merging --- .github/workflows/gh-ci.yaml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 9fbde03..a7238ec 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -64,7 +64,11 @@ jobs: install-tests: false installer: mamba shell: bash -l {0} - + + - name: Install openbabel + run: | + mamba install -c conda-forge openbabel<3.0.0 + - name: Install package run: | python --version @@ -86,8 +90,8 @@ jobs: pytest -n auto -v --cov=mda_openbabel_converter --cov-report=xml --color=yes mda_openbabel_converter/tests/ - name: codecov - if: github.repository == 'lunamorrow/mda_openbabel_converter' && github.event_name != 'schedule' - uses: codecov/codecov-action@v4 + if: github.repository == 'MDAnalysis/mda_openbabel_converter' && github.event_name != 'schedule' + uses: codecov/codecov-action@v3 with: token: ${{ secrets.CODECOV_TOKEN }} file: coverage.xml @@ -96,7 +100,8 @@ jobs: pylint_check: - if: "github.repository == 'MDAnalysis/mda-openbabel-converter'" + if: "github.repository == 'MDAnalysis/mda_openbabel_converter'" + needs: environment-config runs-on: ubuntu-latest steps: From 45a1ce523ec379c38217e9c8e7e11cc88af5c85b Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Thu, 18 Jul 2024 14:50:21 +1000 Subject: [PATCH 08/14] Fixing new error take 8 --- .github/workflows/gh-ci.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index a7238ec..7843208 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -65,6 +65,14 @@ jobs: installer: mamba shell: bash -l {0} + - name: Setup Conda Environment + uses: mamba-org/setup-micromamba@v1 + with: + environment-file: devtools/conda-envs/test_env.yml + environment-name: mda-ob + create-args: >- + python==${{ matrix.python-version }} + - name: Install openbabel run: | mamba install -c conda-forge openbabel<3.0.0 From d5d82af1d72d7ab2c8a12e98b9aa5cf717d6f655 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Thu, 18 Jul 2024 14:50:21 +1000 Subject: [PATCH 09/14] Fixing new error take 8 and some more From d8219e1802a8fa5ebb56bb7399a998e52d01c58c Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Wed, 24 Jul 2024 13:23:31 +1000 Subject: [PATCH 10/14] include env setup --- .github/workflows/gh-ci.yaml | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index 7843208..d3b57ea 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -65,23 +65,22 @@ jobs: installer: mamba shell: bash -l {0} + - name: Install openbabel + run: | + mamba install -c conda-forge 'openbabel<3.0.0' + - name: Setup Conda Environment uses: mamba-org/setup-micromamba@v1 with: - environment-file: devtools/conda-envs/test_env.yml + environment-file: devtools/conda-envs/test_env.yaml environment-name: mda-ob create-args: >- python==${{ matrix.python-version }} - - name: Install openbabel - run: | - mamba install -c conda-forge openbabel<3.0.0 - - name: Install package run: | python --version - mamba install -c conda-forge openbabel<3.0.0 - python -m pip install . --no-deps + python -m pip install . --no-deps - name: Python information run: | From f1870ccb5116ef8fd4bbc424a55395e9be3195c9 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Wed, 24 Jul 2024 12:34:33 +1000 Subject: [PATCH 11/14] final commit before moving to new branch for new PR --- devtools/conda-envs/test_env.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index dc4279b..37b6ccc 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -10,6 +10,9 @@ dependencies: # MDAnalysis - MDAnalysis + # OpenBabel + - openbabel + # Testing - pytest - pytest-cov From bcb48977654a261caad3e657a6bc55f11ea4b228 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Wed, 24 Jul 2024 12:34:33 +1000 Subject: [PATCH 12/14] final commit before moving to new branch for new PR add openbabel dependency From e86b6ceb8acc3c82ca6b9acc8fd23e1e71a4b584 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Wed, 24 Jul 2024 13:28:19 +1000 Subject: [PATCH 13/14] quick fix --- .github/workflows/gh-ci.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index d3b57ea..cb1c80c 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -108,7 +108,6 @@ jobs: pylint_check: if: "github.repository == 'MDAnalysis/mda_openbabel_converter'" - needs: environment-config runs-on: ubuntu-latest steps: From 3710ae46e0eb40db688aac7c340eeed9b06ee325 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Wed, 24 Jul 2024 14:46:33 +1000 Subject: [PATCH 14/14] Allow openbabel version to float and remove seperate install --- .github/workflows/gh-ci.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml index cb1c80c..7079784 100644 --- a/.github/workflows/gh-ci.yaml +++ b/.github/workflows/gh-ci.yaml @@ -65,10 +65,6 @@ jobs: installer: mamba shell: bash -l {0} - - name: Install openbabel - run: | - mamba install -c conda-forge 'openbabel<3.0.0' - - name: Setup Conda Environment uses: mamba-org/setup-micromamba@v1 with: