From 11de58f39a9c8679c9225e420b40a7e2cc507717 Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Thu, 20 Jun 2024 14:38:03 -0600 Subject: [PATCH 01/12] add python 3.12 and macOS-13 to test matrix --- .github/workflows/CI.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 4cac0ab4..b4ae9ddc 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -18,8 +18,8 @@ jobs: strategy: fail-fast: false matrix: - os: [macOS-latest, ubuntu-latest, windows-latest] - python-version: ["3.9", "3.10", "3.11"] + os: [macOS-latest, macOS-13, ubuntu-latest, windows-latest] + python-version: ["3.9", "3.10", "3.11", "3.12"] exclude: - os: windows-latest python-version: "3.9" From 5341884fd5d2da99884a4f07e760e18c3e16ac47 Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Thu, 20 Jun 2024 14:45:33 -0600 Subject: [PATCH 02/12] change minimum python version to 3.9 in yml files --- environment-dev-win.yml | 2 +- environment-dev.yml | 2 +- environment.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/environment-dev-win.yml b/environment-dev-win.yml index 4517b5b7..9d0ee546 100644 --- a/environment-dev-win.yml +++ b/environment-dev-win.yml @@ -19,6 +19,6 @@ dependencies: - pytest-cov - pytest-timeout - pytest-xdist - - python>=3.8 + - python>=3.9 - requests - requests-mock diff --git a/environment-dev.yml b/environment-dev.yml index b78320fa..e2852dd9 100644 --- a/environment-dev.yml +++ b/environment-dev.yml @@ -22,6 +22,6 @@ dependencies: - pytest-cov - pytest-timeout - pytest-xdist - - python>=3.8 + - python>=3.9 - requests - requests-mock diff --git a/environment.yml b/environment.yml index f1e9302e..59d7a4e9 100644 --- a/environment.yml +++ b/environment.yml @@ -10,4 +10,4 @@ dependencies: - parmed>=3.4.3 - ele - requests - - python>=3.8 + - python>=3.9 From 23649ec0d8e4283201260f87bcc724811e400e88 Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Thu, 20 Jun 2024 14:47:56 -0600 Subject: [PATCH 03/12] change overlap in packmol args --- foyer/tests/test_forcefield.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/foyer/tests/test_forcefield.py b/foyer/tests/test_forcefield.py index b64cbf03..64e6a1ab 100644 --- a/foyer/tests/test_forcefield.py +++ b/foyer/tests/test_forcefield.py @@ -684,7 +684,12 @@ def test_no_overlap_residue_atom_overlap(self): mol1.name = "CCC" mol2.name = "COC" - box = mb.fill_box([mol1, mol2], n_compounds=[2, 2], density=700) + box = mb.fill_box( + [mol1, mol2], + n_compounds=[2, 2], + overlap=0.01, + density=700 + ) all_substructures = [] structure = box.to_parmed(residues=["CCC", "COC"]) From 104bb3fc67813aabccdea159f7775ca8c3bb333b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 20 Jun 2024 20:49:01 +0000 Subject: [PATCH 04/12] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- foyer/tests/test_forcefield.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/foyer/tests/test_forcefield.py b/foyer/tests/test_forcefield.py index 64e6a1ab..2e9ad6ca 100644 --- a/foyer/tests/test_forcefield.py +++ b/foyer/tests/test_forcefield.py @@ -685,10 +685,7 @@ def test_no_overlap_residue_atom_overlap(self): mol2.name = "COC" box = mb.fill_box( - [mol1, mol2], - n_compounds=[2, 2], - overlap=0.01, - density=700 + [mol1, mol2], n_compounds=[2, 2], overlap=0.01, density=700 ) all_substructures = [] From a81c2a33cb233c315f5625624116247afa9471f5 Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Thu, 20 Jun 2024 14:50:51 -0600 Subject: [PATCH 05/12] update py version in windows yml file --- environment-win.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment-win.yml b/environment-win.yml index f7ba8545..cc6a7090 100644 --- a/environment-win.yml +++ b/environment-win.yml @@ -6,7 +6,7 @@ dependencies: - lark-parser - lxml - networkx>=2.5 - - openmm>=7.6 + - openmm - parmed>=3.4.3 - ele - requests @@ -16,4 +16,4 @@ dependencies: - pytest-cov - pytest-timeout - pytest-xdist - - python<=3.8 + - python>=3.9 From ff19fd1b825e4990ca9dbb1ffd586bd9c7ef00be Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Thu, 20 Jun 2024 14:59:45 -0600 Subject: [PATCH 06/12] bleeding edge tests was not installing hoomd, but needs it for GMSO tests --- .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 b4ae9ddc..40d46531 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -75,7 +75,7 @@ jobs: uses: mamba-org/setup-micromamba@v1 with: environment-file: environment-dev.yml - create-args: python=3.10 + create-args: python=3.12 - name: Clone mBuild and GMSO run: | git clone https://github.com/mosdef-hub/mbuild.git @@ -85,6 +85,7 @@ jobs: run: | micromamba update --name foyer-dev --file mbuild/environment.yml micromamba update --name foyer-dev --file gmso/environment.yml + micromamba install -c conda-forge hoomd - name: Install Packages from Source run: | From 60845b3d8e781c38d05cf78c4b39c8e742215cd7 Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Thu, 20 Jun 2024 15:11:35 -0600 Subject: [PATCH 07/12] pin mbuild to >0.17 so python 3.12 tests don't fail --- environment-dev-win.yml | 2 +- environment-dev.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/environment-dev-win.yml b/environment-dev-win.yml index 9d0ee546..4f8d70ce 100644 --- a/environment-dev-win.yml +++ b/environment-dev-win.yml @@ -7,7 +7,7 @@ dependencies: - codecov - lark-parser - lxml - - mbuild + - mbuild>=0.17 - treelib - gmso - networkx>=2.5 diff --git a/environment-dev.yml b/environment-dev.yml index e2852dd9..0485ab36 100644 --- a/environment-dev.yml +++ b/environment-dev.yml @@ -6,7 +6,7 @@ dependencies: - codecov - lark-parser - lxml - - mbuild + - mbuild>=0.17 - treelib - gmso - networkx>=2.5 From 51530470c5b108799ceb2a18834fd272b2d2f8ee Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Fri, 21 Jun 2024 13:09:18 -0600 Subject: [PATCH 08/12] Fix bonding in custom ethane pdb file --- foyer/tests/files/ethane_customtype.pdb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/foyer/tests/files/ethane_customtype.pdb b/foyer/tests/files/ethane_customtype.pdb index 1ec2b7ee..404dc198 100644 --- a/foyer/tests/files/ethane_customtype.pdb +++ b/foyer/tests/files/ethane_customtype.pdb @@ -9,7 +9,9 @@ ATOM 5 _Hb ETH 1 2.956 1.278 -9.381 0.00 0.00 H ATOM 6 _Hb ETH 1 4.748 0.049 -7.277 0.00 0.00 H ATOM 7 _Hb ETH 1 5.187 0.312 -8.947 0.00 0.00 H ATOM 8 _Hb ETH 1 4.890 1.676 -7.897 0.00 0.00 H -CONECT 1 2 +CONECT 1 2 3 4 5 6 7 8 +CONECT 2 1 6 7 8 +CONECT 1 2 CONECT 1 3 CONECT 1 4 CONECT 1 5 From 7e719d40c8704ca84941d319828bc9494e2b41b9 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 21 Jun 2024 19:09:34 +0000 Subject: [PATCH 09/12] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- foyer/tests/files/ethane_customtype.pdb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/foyer/tests/files/ethane_customtype.pdb b/foyer/tests/files/ethane_customtype.pdb index 404dc198..6155e140 100644 --- a/foyer/tests/files/ethane_customtype.pdb +++ b/foyer/tests/files/ethane_customtype.pdb @@ -11,7 +11,7 @@ ATOM 7 _Hb ETH 1 5.187 0.312 -8.947 0.00 0.00 H ATOM 8 _Hb ETH 1 4.890 1.676 -7.897 0.00 0.00 H CONECT 1 2 3 4 5 6 7 8 CONECT 2 1 6 7 8 -CONECT 1 2 +CONECT 1 2 CONECT 1 3 CONECT 1 4 CONECT 1 5 From 6a55c3afd9db482a8ac3996e202e95114913ad08 Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Fri, 21 Jun 2024 13:41:11 -0600 Subject: [PATCH 10/12] remove hoomd install from bleeding test workflow, not needed --- .github/workflows/CI.yaml | 1 - foyer/tests/files/ethane_customtype.pdb | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 40d46531..9e7a1974 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -85,7 +85,6 @@ jobs: run: | micromamba update --name foyer-dev --file mbuild/environment.yml micromamba update --name foyer-dev --file gmso/environment.yml - micromamba install -c conda-forge hoomd - name: Install Packages from Source run: | diff --git a/foyer/tests/files/ethane_customtype.pdb b/foyer/tests/files/ethane_customtype.pdb index 6155e140..96e11e48 100644 --- a/foyer/tests/files/ethane_customtype.pdb +++ b/foyer/tests/files/ethane_customtype.pdb @@ -9,7 +9,7 @@ ATOM 5 _Hb ETH 1 2.956 1.278 -9.381 0.00 0.00 H ATOM 6 _Hb ETH 1 4.748 0.049 -7.277 0.00 0.00 H ATOM 7 _Hb ETH 1 5.187 0.312 -8.947 0.00 0.00 H ATOM 8 _Hb ETH 1 4.890 1.676 -7.897 0.00 0.00 H -CONECT 1 2 3 4 5 6 7 8 +CONECT 1 2 3 4 5 CONECT 2 1 6 7 8 CONECT 1 2 CONECT 1 3 From 27665722b6613a4cdd3dd7db95beed01e1be8638 Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Tue, 25 Jun 2024 13:06:26 -0600 Subject: [PATCH 11/12] only test py versions on ubuntu, test arch versions on py3.12 --- .github/workflows/CI.yaml | 54 +++++++++++++++++++++++++++++---------- 1 file changed, 40 insertions(+), 14 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 9e7a1974..55fc0261 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -11,18 +11,15 @@ on: - cron: "0 0 * * *" jobs: - test: + python-test: if: github.event.pull_request.draft == false - name: Foyer Tests + name: Foyer Tests (python) runs-on: ${{ matrix.os }} strategy: fail-fast: false matrix: - os: [macOS-latest, macOS-13, ubuntu-latest, windows-latest] + os: [ubuntu-latest] python-version: ["3.9", "3.10", "3.11", "3.12"] - exclude: - - os: windows-latest - python-version: "3.9" defaults: run: @@ -37,14 +34,6 @@ jobs: with: environment-file: environment-dev.yml create-args: python=${{ matrix.python-version }} - if: runner.os != 'Windows' - - - name: Install Mamba (Windows) - uses: mamba-org/setup-micromamba@v1 - with: - environment-file: environment-dev-win.yml - create-args: python=${{ matrix.python-version }} - if: runner.os == 'Windows' - name: Install Package run: python -m pip install -e . @@ -58,6 +47,43 @@ jobs: name: Foyer-Coverage verbose: true files: ./coverage.xml + os-test: + if: github.event.pull_request.draft == false + name: Foyer Tests (arch) + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + os: [macOS-latest, macOS-13, ubuntu-latest, windows-latest] + python-version: ["3.12"] + + defaults: + run: + shell: bash -l {0} + + steps: + - uses: actions/checkout@v3 + name: Checkout Branch / Pull Request + + - name: Install Mamba (Linux) + uses: mamba-org/setup-micromamba@v1 + with: + environment-file: environment-dev.yml + create-args: python=${{ matrix.python-version }} + if: runner.os != 'Windows' + + - name: Install Mamba (Windows) + uses: mamba-org/setup-micromamba@v1 + with: + environment-file: environment-dev-win.yml + create-args: python=${{ matrix.python-version }} + if: runner.os == 'Windows' + + - name: Install Package + run: python -m pip install -e . + + - name: Test (OS -> ${{ matrix.os }} / Python -> ${{ matrix.python-version }}) + run: python -m pytest -v -nauto --color yes --pyargs foyer bleeding-edge-test: if: github.event.pull_request.draft == false From b2346b271d6ec73e1dc2749f6091a7e8652073d6 Mon Sep 17 00:00:00 2001 From: chrisjonesBSU Date: Tue, 25 Jun 2024 15:35:07 -0600 Subject: [PATCH 12/12] try to fix formatting --- .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 55fc0261..049ff98e 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -11,7 +11,7 @@ on: - cron: "0 0 * * *" jobs: - python-test: + test: if: github.event.pull_request.draft == false name: Foyer Tests (python) runs-on: ${{ matrix.os }} @@ -47,7 +47,8 @@ jobs: name: Foyer-Coverage verbose: true files: ./coverage.xml - os-test: + + arch-test: if: github.event.pull_request.draft == false name: Foyer Tests (arch) runs-on: ${{ matrix.os }}