From e28bd4705d14c5e10ae91c4bac1c6008f85e2e43 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 09:43:47 -0800 Subject: [PATCH 01/13] include gufe main and latest in ci matrix --- .github/workflows/ci.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index fc039385d..9468c010b 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -30,7 +30,7 @@ defaults: jobs: tests: runs-on: ${{ matrix.os }} - name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🗃️${{ matrix.pydantic-version }} oechem: ${{ matrix.openeye }}" + name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🗃️${{ matrix.pydantic-version }} oechem: ${{ matrix.openeye }} gufe: ${{matrix.gufe-version}}" strategy: fail-fast: false matrix: @@ -41,6 +41,7 @@ jobs: - "3.11" - "3.12" openeye: ["no"] + gufe-version: ['latest', 'main'] include: - os: "macos-latest" python-version: "3.12" @@ -96,8 +97,8 @@ jobs: micromamba install -c openeye openeye-toolkits python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'oechem license check failed!'" - - name: "Install GUFE from main@HEAD" - run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main + - name: "Install GUFE from ${matrix.gufe-version}" + run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@${matrix.gufe-version} - name: "Install" run: python -m pip install --no-deps -e . From fbdd62ab82efd7ba93ca55f0039a7b8de9389a12 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 09:58:33 -0800 Subject: [PATCH 02/13] fixing syntax --- .github/workflows/ci.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 9468c010b..24d8d2f0b 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -30,7 +30,7 @@ defaults: jobs: tests: runs-on: ${{ matrix.os }} - name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🗃️${{ matrix.pydantic-version }} oechem: ${{ matrix.openeye }} gufe: ${{matrix.gufe-version}}" + name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }} 🗃️${{ matrix.pydantic-version }} oechem-${{ matrix.openeye }} gufe-${{ matrix.gufe-version }}" strategy: fail-fast: false matrix: @@ -97,8 +97,8 @@ jobs: micromamba install -c openeye openeye-toolkits python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'oechem license check failed!'" - - name: "Install GUFE from ${matrix.gufe-version}" - run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@${matrix.gufe-version} + - name: "Install GUFE from ${{ matrix.gufe-version }}" + run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@${{ matrix.gufe-version }} - name: "Install" run: python -m pip install --no-deps -e . From b553bfbf7d1d30e8a77ff497500588fdb9d88fd2 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 10:11:46 -0800 Subject: [PATCH 03/13] specify gufe 1.1.0 --- .github/workflows/ci.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 24d8d2f0b..9c8733a58 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -41,7 +41,7 @@ jobs: - "3.11" - "3.12" openeye: ["no"] - gufe-version: ['latest', 'main'] + gufe-version: ['v1.1.0', 'main'] include: - os: "macos-latest" python-version: "3.12" From ecc8cf17f62d46bc0c827b622da30305a3243588 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 10:40:27 -0800 Subject: [PATCH 04/13] specifying v1.1.0 --- .github/workflows/ci.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 9c8733a58..74b06eb6c 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -41,23 +41,27 @@ jobs: - "3.11" - "3.12" openeye: ["no"] - gufe-version: ['v1.1.0', 'main'] + gufe-version: ['v1.1.0', 'dev'] include: - os: "macos-latest" python-version: "3.12" pydantic-version: ">1" + gufe-version: 'v1.1.0' - os: "ubuntu-latest" python-version: "3.11" pydantic-version: "<2" + gufe-version: 'v1.1.0' - os: "ubuntu-latest" python-version: "3.11" pydantic-version: ">1" openeye: "yes" + gufe-version: 'v1.1.0' - os: "macos-latest" python-version: "3.12" pydantic-version: ">1" omff-version: ">0.13" openeye: ["no"] + gufe-version: 'v1.1.0' env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt From eecbb9d137bccb3d920e6e759b1a87b5f6b6d4c2 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 10:46:31 -0800 Subject: [PATCH 05/13] install gufe from conda-forge if latest --- .github/workflows/ci.yaml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 74b06eb6c..71c839230 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -41,27 +41,27 @@ jobs: - "3.11" - "3.12" openeye: ["no"] - gufe-version: ['v1.1.0', 'dev'] + gufe-version: ['latest', 'dev'] include: - os: "macos-latest" python-version: "3.12" pydantic-version: ">1" - gufe-version: 'v1.1.0' + gufe-version: 'latest' - os: "ubuntu-latest" python-version: "3.11" pydantic-version: "<2" - gufe-version: 'v1.1.0' + gufe-version: 'latest' - os: "ubuntu-latest" python-version: "3.11" pydantic-version: ">1" openeye: "yes" - gufe-version: 'v1.1.0' + gufe-version: 'latest' - os: "macos-latest" python-version: "3.12" pydantic-version: ">1" omff-version: ">0.13" openeye: ["no"] - gufe-version: 'v1.1.0' + gufe-version: 'latest' env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt @@ -101,8 +101,9 @@ jobs: micromamba install -c openeye openeye-toolkits python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'oechem license check failed!'" - - name: "Install GUFE from ${{ matrix.gufe-version }}" - run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@${{ matrix.gufe-version }} + - name: "Install latest released version of GUFE." # the default environment installs from gufe@main + if: ${{ matrix.gufe-version == 'latest' }} + run: micromamba install gufe - name: "Install" run: python -m pip install --no-deps -e . From b322db0f5e5dcd5552887421017a499e30d48223 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 11:05:13 -0800 Subject: [PATCH 06/13] try force reintalling to get gufe latest --- .github/workflows/ci.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 71c839230..41f0bad1e 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -101,9 +101,10 @@ jobs: micromamba install -c openeye openeye-toolkits python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'oechem license check failed!'" - - name: "Install latest released version of GUFE." # the default environment installs from gufe@main + - name: "Install latest released version of GUFE." if: ${{ matrix.gufe-version == 'latest' }} - run: micromamba install gufe + # the default environment installs from gufe@main, so we need to reinstall here + run: micromamba install gufe --force-reinstall - name: "Install" run: python -m pip install --no-deps -e . From f2821f6cfb848ec7020365e59007180cfbd311d4 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 11:30:15 -0800 Subject: [PATCH 07/13] switch to use conda-forge gufe in environment yaml --- .github/workflows/ci.yaml | 10 ++++------ environment.yml | 2 +- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 41f0bad1e..d1e0c226c 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -76,9 +76,8 @@ jobs: run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" - name: "Setup Micromamba" - uses: mamba-org/setup-micromamba@v1 + uses: mamba-org/setup-micromamba@v2 with: - micromamba-version: '1.5.6-0' micromamba-binary-path: ~/.local/bin/micromamba environment-file: environment.yml environment-name: openfe_env @@ -101,10 +100,9 @@ jobs: micromamba install -c openeye openeye-toolkits python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'oechem license check failed!'" - - name: "Install latest released version of GUFE." - if: ${{ matrix.gufe-version == 'latest' }} - # the default environment installs from gufe@main, so we need to reinstall here - run: micromamba install gufe --force-reinstall + - name: "Install dev version of GUFE." + if: ${{ matrix.gufe-version == 'dev' }} + run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main - name: "Install" run: python -m pip install --no-deps -e . diff --git a/environment.yml b/environment.yml index 259518f60..9712348fa 100644 --- a/environment.yml +++ b/environment.yml @@ -3,6 +3,7 @@ channels: - conda-forge dependencies: - duecredit<0.10 + - gufe>=1.1.0 - kartograf>=1.0.0 - lomap2>=3.0.0 - numpy @@ -44,4 +45,3 @@ dependencies: - pip: - sphinx-toolbox - openff-nagl-models>=0.1.2 - - git+https://github.com/OpenFreeEnergy/gufe@main From b0b3038eafdbe84e577203356f40365d3714eac1 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 13:22:44 -0800 Subject: [PATCH 08/13] back to micromamba v1 --- .github/workflows/ci.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index d1e0c226c..9a1df726d 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -76,8 +76,9 @@ jobs: run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" - name: "Setup Micromamba" - uses: mamba-org/setup-micromamba@v2 + uses: mamba-org/setup-micromamba@v1 with: + micromamba-version: '1.5.6-0' micromamba-binary-path: ~/.local/bin/micromamba environment-file: environment.yml environment-name: openfe_env From 59feef61bd5c0a3caab33bc1820162163fb02c99 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 13:35:11 -0800 Subject: [PATCH 09/13] bump micromamba to v2 --- .github/workflows/ci.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 9a1df726d..abf134c72 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -76,10 +76,8 @@ jobs: run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" - name: "Setup Micromamba" - uses: mamba-org/setup-micromamba@v1 + uses: mamba-org/setup-micromamba@v2 with: - micromamba-version: '1.5.6-0' - micromamba-binary-path: ~/.local/bin/micromamba environment-file: environment.yml environment-name: openfe_env cache-environment: true From 3057bf7433fa042dcd6b284b56f32991a8704b3e Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 13:40:08 -0800 Subject: [PATCH 10/13] Revert "bump micromamba to v2" This reverts commit 59feef61bd5c0a3caab33bc1820162163fb02c99. --- .github/workflows/ci.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index abf134c72..9a1df726d 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -76,8 +76,10 @@ jobs: run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" - name: "Setup Micromamba" - uses: mamba-org/setup-micromamba@v2 + uses: mamba-org/setup-micromamba@v1 with: + micromamba-version: '1.5.6-0' + micromamba-binary-path: ~/.local/bin/micromamba environment-file: environment.yml environment-name: openfe_env cache-environment: true From 039015e4a1724176fab0bceb25fa27b14a34c48d Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 5 Dec 2024 14:49:36 -0800 Subject: [PATCH 11/13] switch one-offs to test against gufe main --- .github/workflows/ci.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 9a1df726d..7c343ccc8 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -46,22 +46,22 @@ jobs: - os: "macos-latest" python-version: "3.12" pydantic-version: ">1" - gufe-version: 'latest' + gufe-version: 'dev' - os: "ubuntu-latest" python-version: "3.11" pydantic-version: "<2" - gufe-version: 'latest' + gufe-version: 'dev' - os: "ubuntu-latest" python-version: "3.11" pydantic-version: ">1" openeye: "yes" - gufe-version: 'latest' + gufe-version: 'dev' - os: "macos-latest" python-version: "3.12" pydantic-version: ">1" omff-version: ">0.13" openeye: ["no"] - gufe-version: 'latest' + gufe-version: 'dev' env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt From 9bc9cf8c11a5d634257c798ecb02765f582a6cd8 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 6 Dec 2024 09:05:24 -0800 Subject: [PATCH 12/13] use gufe main --- .github/workflows/ci.yaml | 16 ++++++++-------- environment.yml | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 7c343ccc8..8fab45c68 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -41,27 +41,27 @@ jobs: - "3.11" - "3.12" openeye: ["no"] - gufe-version: ['latest', 'dev'] + gufe-version: ['main'] include: - os: "macos-latest" python-version: "3.12" pydantic-version: ">1" - gufe-version: 'dev' + gufe-version: 'main' - os: "ubuntu-latest" python-version: "3.11" pydantic-version: "<2" - gufe-version: 'dev' + gufe-version: 'main' - os: "ubuntu-latest" python-version: "3.11" pydantic-version: ">1" openeye: "yes" - gufe-version: 'dev' + gufe-version: 'main' - os: "macos-latest" python-version: "3.12" pydantic-version: ">1" omff-version: ">0.13" openeye: ["no"] - gufe-version: 'dev' + gufe-version: 'main' env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt @@ -101,9 +101,9 @@ jobs: micromamba install -c openeye openeye-toolkits python -c "import openeye; assert openeye.oechem.OEChemIsLicensed(), 'oechem license check failed!'" - - name: "Install dev version of GUFE." - if: ${{ matrix.gufe-version == 'dev' }} - run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main + - name: "Install GUFE at {{ matrix.gufe-version }}" + if: ${{ matrix.gufe-version != 'main' }} + run: python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@${{ matrix.gufe-version }} - name: "Install" run: python -m pip install --no-deps -e . diff --git a/environment.yml b/environment.yml index 9712348fa..01b758334 100644 --- a/environment.yml +++ b/environment.yml @@ -3,7 +3,6 @@ channels: - conda-forge dependencies: - duecredit<0.10 - - gufe>=1.1.0 - kartograf>=1.0.0 - lomap2>=3.0.0 - numpy @@ -45,3 +44,4 @@ dependencies: - pip: - sphinx-toolbox - openff-nagl-models>=0.1.2 + - git+https://github.com/OpenFreeEnergy/gufe@main \ No newline at end of file From cb25ce505de1fe43fa3ba7375a71444423e1a369 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 6 Dec 2024 09:16:49 -0800 Subject: [PATCH 13/13] pin to a9b5 --- .github/workflows/ci.yaml | 15 +++++++++++---- environment.yml | 2 +- 2 files changed, 12 insertions(+), 5 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 8fab45c68..2a54bd2e7 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -41,26 +41,33 @@ jobs: - "3.11" - "3.12" openeye: ["no"] - gufe-version: ['main'] + gufe-version: ['a9b5982471eb3644ca8c4423c7001e6309a3f544'] include: - os: "macos-latest" python-version: "3.12" pydantic-version: ">1" - gufe-version: 'main' + gufe-version: 'a9b5982471eb3644ca8c4423c7001e6309a3f544' - os: "ubuntu-latest" python-version: "3.11" pydantic-version: "<2" - gufe-version: 'main' + gufe-version: 'a9b5982471eb3644ca8c4423c7001e6309a3f544' - os: "ubuntu-latest" python-version: "3.11" pydantic-version: ">1" openeye: "yes" - gufe-version: 'main' + gufe-version: 'a9b5982471eb3644ca8c4423c7001e6309a3f544' - os: "macos-latest" python-version: "3.12" pydantic-version: ">1" omff-version: ">0.13" openeye: ["no"] + gufe-version: 'a9b5982471eb3644ca8c4423c7001e6309a3f544' + + # temporary test against gufe main while we're pinned to a9b5 + - os: "ubuntu-latest" + python-version: "3.11" + pydantic-version: ">1" + openeye: "yes" gufe-version: 'main' env: diff --git a/environment.yml b/environment.yml index 01b758334..259518f60 100644 --- a/environment.yml +++ b/environment.yml @@ -44,4 +44,4 @@ dependencies: - pip: - sphinx-toolbox - openff-nagl-models>=0.1.2 - - git+https://github.com/OpenFreeEnergy/gufe@main \ No newline at end of file + - git+https://github.com/OpenFreeEnergy/gufe@main