From eadcf2ea18373736cb99d9fb65b27e0af1d7279d Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 21 Aug 2024 12:06:44 -0500 Subject: [PATCH 01/21] Add more tests --- .github/workflows/full-stack.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 947f59e..4ea9821 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -95,6 +95,7 @@ jobs: openff-qcsubmit/ \ openff-units/ \ openff-models/ \ + openff-fragmenter/ \ smirnoff-plugins/ - name: Run 'everything all at once' tests @@ -102,6 +103,9 @@ jobs: python -m pytest $PYTEST_ARGS \ smirnoff-plugins/smirnoff_plugins/_tests/ \ openff-interchange/openff/interchange/_tests/ \ + openff-models/openff/models/_tests/ \ + openff-units/openff/models/_tests/ \ + openff-fragmenter/openff/fragmenter/_tests/ \ --ignore=smirnoff-plugins/smirnoff_plugins/_tests/handlers/test_nonbonded.py \ --ignore=openff-interchange/openff/interchange/_tests/unit_tests/components/test_packmol.py \ --ignore=openff-interchange/openff/interchange/_tests/test_parameter_plugins.py::test_force_field_custom_handler \ From 0f154db32943b3656476b4fc6abb99f6ee218860 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 21 Aug 2024 12:54:58 -0500 Subject: [PATCH 02/21] Use branch of Fragmenter --- .github/workflows/full-stack.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 4ea9821..c73320d 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -54,6 +54,7 @@ jobs: with: repository: openforcefield/openff-fragmenter path: openff-fragmenter + ref: no-duplicate-runslow - name: Checkout SMIRNOFF plugins uses: actions/checkout@v4 From 757b8f43224b1144b0a6fdebede69a739bfcdffc Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 21 Aug 2024 13:26:28 -0500 Subject: [PATCH 03/21] Typo --- .github/workflows/full-stack.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index c73320d..185cbc2 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -105,7 +105,7 @@ jobs: smirnoff-plugins/smirnoff_plugins/_tests/ \ openff-interchange/openff/interchange/_tests/ \ openff-models/openff/models/_tests/ \ - openff-units/openff/models/_tests/ \ + openff-units/openff/units/_tests/ \ openff-fragmenter/openff/fragmenter/_tests/ \ --ignore=smirnoff-plugins/smirnoff_plugins/_tests/handlers/test_nonbonded.py \ --ignore=openff-interchange/openff/interchange/_tests/unit_tests/components/test_packmol.py \ From 568ebb271902ecd21a3cfd53722cbee32f006710 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 21 Aug 2024 13:37:05 -0500 Subject: [PATCH 04/21] Add back toolkit tests to see what fails --- .github/workflows/full-stack.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 185cbc2..ec1d1bd 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -103,6 +103,7 @@ jobs: run: | python -m pytest $PYTEST_ARGS \ smirnoff-plugins/smirnoff_plugins/_tests/ \ + openff-toolkit/openff/toolkit/_tests/ \ openff-interchange/openff/interchange/_tests/ \ openff-models/openff/models/_tests/ \ openff-units/openff/units/_tests/ \ From 1086562295633e1e57fd5ac1bc24399790175f4e Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Tue, 27 Aug 2024 16:16:29 -0500 Subject: [PATCH 05/21] Kick tests --- .github/workflows/full-stack.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index ec1d1bd..65fe66f 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -27,7 +27,7 @@ jobs: env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt - PYTEST_ARGS: -n logical --rootdir=. --durations=20 + PYTEST_ARGS: -n logical --rootdir=. --durations=20 -v steps: - uses: actions/checkout@v4 From 46b992e0218874aad9b41f1de713ab643d4d1d3c Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 09:05:48 -0600 Subject: [PATCH 06/21] Update --- .github/workflows/full-stack.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 1481af8..fd3d113 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -101,7 +101,7 @@ jobs: - name: Run 'everything all at once' tests run: | - python -m pytest $PYTEST_ARGS -m "not leaky" \ + python -m pytest $PYTEST_ARGS \ smirnoff-plugins/smirnoff_plugins/_tests/ \ openff-toolkit/openff/toolkit/_tests/ \ openff-interchange/openff/interchange/_tests/ \ From f9201650205fffa4529b00cfaa7c3d070c2c6719 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 09:09:39 -0600 Subject: [PATCH 07/21] Fail fast --- .github/workflows/full-stack.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index fd3d113..0548baf 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -15,11 +15,10 @@ jobs: runs-on: ${{ matrix.os }} strategy: - fail-fast: false matrix: os: - "ubuntu-latest" - - "macos-latest" # this is probably macos-14 + - "macos-latest" python-version: - "3.10" - "3.11" From 59020a9e7af3b77c6ed2de46082d497d95a88546 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 09:15:33 -0600 Subject: [PATCH 08/21] Debug --- .github/workflows/full-stack.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 0548baf..74c3001 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -26,7 +26,7 @@ jobs: env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt - PYTEST_ARGS: -x -n logical --rootdir=. --durations=20 + PYTEST_ARGS: -x -n logical --durations=20 steps: - uses: actions/checkout@v4 From efd1cba5bd821a2a512084fa4633ab10a0460f0a Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 09:18:52 -0600 Subject: [PATCH 09/21] Debug --- .github/workflows/full-stack.yaml | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 74c3001..297dde6 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -100,14 +100,7 @@ jobs: - name: Run 'everything all at once' tests run: | - python -m pytest $PYTEST_ARGS \ - smirnoff-plugins/smirnoff_plugins/_tests/ \ - openff-toolkit/openff/toolkit/_tests/ \ - openff-interchange/openff/interchange/_tests/ \ - openff-fragmenter/openff/fragmenter/_tests/ \ - openff-units/openff/units/_tests/ \ - openff-utilities/openff/utilities/_tests/ \ - --ignore=openff-interchange/openff/interchange/_tests/unit_tests/components/test_packmol.py + python -m pytest $PYTEST_ARGS . - name: Run QC-adjacent tests run: | From d40a4f5deef7b8251704977adf26afd40a346d1d Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 10:05:23 -0600 Subject: [PATCH 10/21] Install "downstream dummy" of units package --- .github/workflows/full-stack.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 297dde6..a8ba51b 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -93,6 +93,7 @@ jobs: openff-interchange/plugins/ \ openff-qcsubmit/ \ openff-units/ \ + openff-units/downstream_dummy/ \ openff-fragmenter/ \ openff-utilities/ \ smirnoff-plugins/ From e015cb7668802846a9cabd08f2f8a2aa6dc25ac3 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 10:09:50 -0600 Subject: [PATCH 11/21] No plugins --- .github/workflows/full-stack.yaml | 7 ------- devtools/conda-envs/full-stack.yaml | 1 - 2 files changed, 8 deletions(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index a8ba51b..29423c5 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -63,12 +63,6 @@ jobs: repository: openforcefield/openff-units path: openff-units - - name: Checkout SMIRNOFF plugins - uses: actions/checkout@v4 - with: - repository: openforcefield/smirnoff-plugins - path: smirnoff-plugins - - name: Checkout OpenFF Utilities uses: actions/checkout@v4 with: @@ -96,7 +90,6 @@ jobs: openff-units/downstream_dummy/ \ openff-fragmenter/ \ openff-utilities/ \ - smirnoff-plugins/ pip list - name: Run 'everything all at once' tests diff --git a/devtools/conda-envs/full-stack.yaml b/devtools/conda-envs/full-stack.yaml index b03bfcc..f1d3c9a 100644 --- a/devtools/conda-envs/full-stack.yaml +++ b/devtools/conda-envs/full-stack.yaml @@ -8,7 +8,6 @@ dependencies: - openff-toolkit - openff-fragmenter - openff-interchange - - smirnoff-plugins - pymbar - pytest - pytest-randomly From c33c8c7bc7699de5143cab8cbee6d3f4318e94f5 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 10:14:28 -0600 Subject: [PATCH 12/21] Typo --- .github/workflows/full-stack.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 29423c5..72943d9 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -89,7 +89,7 @@ jobs: openff-units/ \ openff-units/downstream_dummy/ \ openff-fragmenter/ \ - openff-utilities/ \ + openff-utilities/ pip list - name: Run 'everything all at once' tests From 410fdfcf93aa6cf216da3c595b60d2140ca41e86 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 10:21:58 -0600 Subject: [PATCH 13/21] Skip (known) leaky test --- .github/workflows/full-stack.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 72943d9..ffa0ada 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -100,7 +100,8 @@ jobs: run: | python -m pytest $PYTEST_ARGS \ openff-qcsubmit/openff/qcsubmit/_tests/ \ - --ignore=openff-qcsubmit/openff/qcsubmit/_tests/test_submissions.py + --ignore=openff-qcsubmit/openff/qcsubmit/_tests/test_submissions.py \ + --ignore=openff/utilities/_tests/test_provenance.py::test_conda_unavailable_returns_empty_dict - name: Run NAGL tests via pyargs if: matrix.os == 'FOOBAR' From 6d3e2f2151d5a219af235440368394ccf02eee21 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 10:26:56 -0600 Subject: [PATCH 14/21] Debug --- .github/workflows/full-stack.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index ffa0ada..405248d 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -101,7 +101,7 @@ jobs: python -m pytest $PYTEST_ARGS \ openff-qcsubmit/openff/qcsubmit/_tests/ \ --ignore=openff-qcsubmit/openff/qcsubmit/_tests/test_submissions.py \ - --ignore=openff/utilities/_tests/test_provenance.py::test_conda_unavailable_returns_empty_dict + --ignore=openff/utilities/_tests/test_provenance.py - name: Run NAGL tests via pyargs if: matrix.os == 'FOOBAR' From db6db2182c544a8839074652dacd2b34e987c545 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 10:37:01 -0600 Subject: [PATCH 15/21] Debug --- .github/workflows/full-stack.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 405248d..0ebc095 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -101,7 +101,7 @@ jobs: python -m pytest $PYTEST_ARGS \ openff-qcsubmit/openff/qcsubmit/_tests/ \ --ignore=openff-qcsubmit/openff/qcsubmit/_tests/test_submissions.py \ - --ignore=openff/utilities/_tests/test_provenance.py + --ignore=openff-utilities/openff/utilities/_tests/test_provenance.py - name: Run NAGL tests via pyargs if: matrix.os == 'FOOBAR' From a1919c6bf319f3b1daddef0382dbd446762d7ede Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 10:47:57 -0600 Subject: [PATCH 16/21] Debug --- .github/workflows/full-stack.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 0ebc095..0b0660d 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -94,14 +94,14 @@ jobs: - name: Run 'everything all at once' tests run: | - python -m pytest $PYTEST_ARGS . + python -m pytest $PYTEST_ARGS . \ + --ignore=openff-utilities/openff/utilities/_tests/test_provenance.py - name: Run QC-adjacent tests run: | python -m pytest $PYTEST_ARGS \ openff-qcsubmit/openff/qcsubmit/_tests/ \ - --ignore=openff-qcsubmit/openff/qcsubmit/_tests/test_submissions.py \ - --ignore=openff-utilities/openff/utilities/_tests/test_provenance.py + --ignore=openff-qcsubmit/openff/qcsubmit/_tests/test_submissions.py - name: Run NAGL tests via pyargs if: matrix.os == 'FOOBAR' From 6810a38414e93bb7c42c58c7dd1f4a27925ea921 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 11:09:09 -0600 Subject: [PATCH 17/21] Debug --- .github/workflows/full-stack.yaml | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 0b0660d..7f71bcd 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -26,7 +26,7 @@ jobs: env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt - PYTEST_ARGS: -x -n logical --durations=20 + PYTEST_ARGS: -n logical --durations=20 steps: - uses: actions/checkout@v4 @@ -94,13 +94,21 @@ jobs: - name: Run 'everything all at once' tests run: | - python -m pytest $PYTEST_ARGS . \ + python -m pytest $PYTEST_ARGS \ + openff-toolkit/ \ + openff-interchange/ \ + openff-units/ \ + openff-utilities/ \ + openff-fragmenter/ \ + openff-nagl/ \ + openff-evaluator/ \ --ignore=openff-utilities/openff/utilities/_tests/test_provenance.py - name: Run QC-adjacent tests run: | python -m pytest $PYTEST_ARGS \ - openff-qcsubmit/openff/qcsubmit/_tests/ \ + openff-bespokefit/ \ + openff-qcsubmit/ \ --ignore=openff-qcsubmit/openff/qcsubmit/_tests/test_submissions.py - name: Run NAGL tests via pyargs From e6f032ebf75d737281fb026e1e80699c73855bb5 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 11:20:00 -0600 Subject: [PATCH 18/21] Debug --- .github/workflows/full-stack.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 7f71bcd..7474a9c 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -26,7 +26,7 @@ jobs: env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt - PYTEST_ARGS: -n logical --durations=20 + PYTEST_ARGS: -n logical --rootdir=. --durations=20 steps: - uses: actions/checkout@v4 From 9956f5f6b1e2430754723d75ad5cdd78215e589f Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 11:24:35 -0600 Subject: [PATCH 19/21] Debug --- .github/workflows/full-stack.yaml | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 7474a9c..1729157 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -94,15 +94,9 @@ jobs: - name: Run 'everything all at once' tests run: | - python -m pytest $PYTEST_ARGS \ - openff-toolkit/ \ - openff-interchange/ \ - openff-units/ \ - openff-utilities/ \ - openff-fragmenter/ \ - openff-nagl/ \ - openff-evaluator/ \ - --ignore=openff-utilities/openff/utilities/_tests/test_provenance.py + python -m pytest $PYTEST_ARGS . \ + --ignore=openff-utilities/openff/utilities/_tests/test_provenance.py \ + --ignore=openff-qcsubmit - name: Run QC-adjacent tests run: | From 4f7d0a9ec6d1aa940a7f009070fc97f45dc7ab29 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 11:34:26 -0600 Subject: [PATCH 20/21] Debug --- .github/workflows/full-stack.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 1729157..94cd993 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -26,7 +26,7 @@ jobs: env: OE_LICENSE: ${{ github.workspace }}/oe_license.txt - PYTEST_ARGS: -n logical --rootdir=. --durations=20 + PYTEST_ARGS: -v -n logical --rootdir=. --durations=20 steps: - uses: actions/checkout@v4 @@ -100,7 +100,7 @@ jobs: - name: Run QC-adjacent tests run: | - python -m pytest $PYTEST_ARGS \ + pytest $PYTEST_ARGS \ openff-bespokefit/ \ openff-qcsubmit/ \ --ignore=openff-qcsubmit/openff/qcsubmit/_tests/test_submissions.py From ce8214dc653329590c040222b41233faef16ca3d Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Wed, 11 Dec 2024 12:05:08 -0600 Subject: [PATCH 21/21] Do not look for bespokefit --- .github/workflows/full-stack.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/full-stack.yaml b/.github/workflows/full-stack.yaml index 94cd993..5862f05 100644 --- a/.github/workflows/full-stack.yaml +++ b/.github/workflows/full-stack.yaml @@ -100,8 +100,9 @@ jobs: - name: Run QC-adjacent tests run: | - pytest $PYTEST_ARGS \ - openff-bespokefit/ \ + # rm openff-interchange/ openff-toolkit/ openff-units/ openff-utilities/ + # micromamba install openff-qcsubmit -c conda-forge -y + pytest $PYTEST_ARGS . \ openff-qcsubmit/ \ --ignore=openff-qcsubmit/openff/qcsubmit/_tests/test_submissions.py