From 557eefde21b3859207eae388dbf31098253019a4 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Thu, 30 Oct 2025 12:14:11 -0700 Subject: [PATCH 01/10] Start of workflow to test doc building --- .github/workflows/openfe-doc-build.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index 7b8b044..470a69c 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -11,7 +11,7 @@ jobs: - name: Checkout ExampleNotebooks repository uses: actions/checkout@v4 with: - path: openfe/docs/ + path: openfe/docs/ExampleNotebooks - name: Checkout conda-forge feedstock uses: actions/checkout@v4 From fdb1480fef0ab4db8f3f8a0dc3453c3b1bdc2165 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Thu, 30 Oct 2025 12:19:03 -0700 Subject: [PATCH 02/10] change order of checkout --- .github/workflows/openfe-doc-build.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index 470a69c..4d3d7f2 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -8,17 +8,17 @@ jobs: runs-on: ubuntu-latest steps: - - name: Checkout ExampleNotebooks repository - uses: actions/checkout@v4 - with: - path: openfe/docs/ExampleNotebooks - - name: Checkout conda-forge feedstock uses: actions/checkout@v4 with: repository: OpenFreeEnergy/openfe path: openfe + - name: Checkout ExampleNotebooks repository + uses: actions/checkout@v4 + with: + path: openfe/docs/ExampleNotebooks + - name: Test file layout run: | pwd From a0f76ae27ecc507a5ce0dc64665f8c48b5643175 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Thu, 30 Oct 2025 12:24:53 -0700 Subject: [PATCH 03/10] build the docs --- .github/workflows/openfe-doc-build.yaml | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index 4d3d7f2..bd2ff23 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -18,10 +18,23 @@ jobs: uses: actions/checkout@v4 with: path: openfe/docs/ExampleNotebooks + + - name: Get current date + id: date + run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" - - name: Test file layout + - name: Install doc environment + uses: mamba-org/setup-micromamba@v2 + with: + environment-file: openfe/docs/environment.yaml + cache-environment: true + cache-downloads: true + cache-environment-key: environment-${{ steps.date.outputs.date }} + cache-downloads-key: downloads-${{ steps.date.outputs.date }} + init-shell: bash + + - name: Build the docs run: | - pwd - ls -l - ls -l * - ls -l openfe/docs + cd openfe/docs + make + From 6ec16640ff2bd494e1e558a17d1baa6f05092c8a Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Thu, 30 Oct 2025 12:25:50 -0700 Subject: [PATCH 04/10] use correct default shell + other enhancements --- .github/workflows/openfe-doc-build.yaml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index bd2ff23..14bcea0 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -3,6 +3,14 @@ name: Test openfe doc build on: workflow_dispatch: +concurrency: + group: "${{ github.workflow }}-${{ github.ref }}" + cancel-in-progress: true + +defaults: + run: + shell: bash -leo pipefail {0} + jobs: test-conda-build: runs-on: ubuntu-latest @@ -37,4 +45,3 @@ jobs: run: | cd openfe/docs make - From 429447c6177ab049ce7504da069ff39d41bf67d5 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Thu, 30 Oct 2025 12:28:32 -0700 Subject: [PATCH 05/10] forgot the make target --- .github/workflows/openfe-doc-build.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index 14bcea0..33ef49b 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -44,4 +44,4 @@ jobs: - name: Build the docs run: | cd openfe/docs - make + make html From 26069fa2cc9ae8f1ae45670d1992f826a5151543 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Thu, 30 Oct 2025 12:31:11 -0700 Subject: [PATCH 06/10] install openfe so we can get the version metadata --- .github/workflows/openfe-doc-build.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index 33ef49b..45d16ee 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -43,5 +43,8 @@ jobs: - name: Build the docs run: | + cd openfe + # install so that we can get a version metadata we use in docs + pip install . --no-deps cd openfe/docs make html From 30641659ffaeecd4ae1ee86cd5e5d393f2cac869 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Thu, 30 Oct 2025 12:32:25 -0700 Subject: [PATCH 07/10] silly cd typo --- .github/workflows/openfe-doc-build.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index 45d16ee..4b78713 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -46,5 +46,5 @@ jobs: cd openfe # install so that we can get a version metadata we use in docs pip install . --no-deps - cd openfe/docs + cd docs make html From 1bc479fe0b01cf59277a285c4206a8b25c63382c Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Thu, 30 Oct 2025 12:42:52 -0700 Subject: [PATCH 08/10] see if this breaks the doc build --- openmm_septop/septop_tutorial.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openmm_septop/septop_tutorial.ipynb b/openmm_septop/septop_tutorial.ipynb index e995c2e..c17042d 100644 --- a/openmm_septop/septop_tutorial.ipynb +++ b/openmm_septop/septop_tutorial.ipynb @@ -23,7 +23,7 @@ "id": "23881797-0bd3-408b-9212-ac206d46cd39", "metadata": {}, "source": [ - "" + "" ] }, { From cb11696b8ce5331731ba29d705c73c5f498a57d6 Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Thu, 30 Oct 2025 12:43:04 -0700 Subject: [PATCH 09/10] run on every PR commit --- .github/workflows/openfe-doc-build.yaml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/.github/workflows/openfe-doc-build.yaml b/.github/workflows/openfe-doc-build.yaml index 4b78713..77c334d 100644 --- a/.github/workflows/openfe-doc-build.yaml +++ b/.github/workflows/openfe-doc-build.yaml @@ -2,6 +2,15 @@ name: Test openfe doc build on: workflow_dispatch: + push: + branches: + - main + pull_request: + branches: + - main + schedule: + # nightly tests, 2 am + - cron: "0 2 * * *" concurrency: group: "${{ github.workflow }}-${{ github.ref }}" From cb85f4267cbb197f22d62697494920824523fc2d Mon Sep 17 00:00:00 2001 From: Mike Henry <11765982+mikemhenry@users.noreply.github.com> Date: Thu, 30 Oct 2025 12:49:15 -0700 Subject: [PATCH 10/10] undo break in notebook --- openmm_septop/septop_tutorial.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openmm_septop/septop_tutorial.ipynb b/openmm_septop/septop_tutorial.ipynb index c17042d..e995c2e 100644 --- a/openmm_septop/septop_tutorial.ipynb +++ b/openmm_septop/septop_tutorial.ipynb @@ -23,7 +23,7 @@ "id": "23881797-0bd3-408b-9212-ac206d46cd39", "metadata": {}, "source": [ - "" + "" ] }, {