From 81e4e46ee6a29fbd481fb1e822bd2fd65d4a99d4 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 14:53:45 -0800 Subject: [PATCH 01/20] don't re-execute tutorials when building docs --- docs/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index aec47aa4..620271f0 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -51,8 +51,8 @@ # Disable notebook timeout nbsphinx_timeout = -1 -# Always re-run notebooks when building docss -nbsphinx_execute = "always" +# Only re-run notebooks that have no outputs +nbsphinx_execute = "auto" # Allow notebook errors nbsphinx_allow_errors = False From 3cd6899a8981c47b5283c934a7bde6a1f7f64741 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 14:53:59 -0800 Subject: [PATCH 02/20] add separate workflow to run notebooks --- .github/workflows/run-notebooks.yml | 36 +++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 .github/workflows/run-notebooks.yml diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml new file mode 100644 index 00000000..2045d5e0 --- /dev/null +++ b/.github/workflows/run-notebooks.yml @@ -0,0 +1,36 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions + +name: CI tests + +on: + push: + branches: + - main # only rerun tutorials when making PRs or changing main + - v3 + pull_request: + branches: + - '*' + +jobs: + build: + + runs-on: macos-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.8", "3.9", "3.11"] + + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + - name: Run tutorial notebooks + run: | + jupyter execute "{}/../docs/tutorials/*.ipynb".format(tests_dir) + From b0346ea93d1d2b0802de17fcc4b0d3a5c01412d2 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 14:55:44 -0800 Subject: [PATCH 03/20] new workflow should prob have its own name --- .github/workflows/run-notebooks.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 2045d5e0..0db31679 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -1,6 +1,4 @@ -# This workflow will install Python dependencies, run tests and lint with a variety of Python versions - -name: CI tests +name: Test jupyter notebook tutorials on: push: From d3b396a2a4e8aed2cd5a53215237326dd68e65f8 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 14:57:03 -0800 Subject: [PATCH 04/20] fix syntax error in workflow --- .github/workflows/run-notebooks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 0db31679..0200665b 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -30,5 +30,5 @@ jobs: if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: Run tutorial notebooks run: | - jupyter execute "{}/../docs/tutorials/*.ipynb".format(tests_dir) + jupyter execute docs/tutorials/*.ipynb From 177728a8b6a88002a688bc32b2a99780641fe480 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 15:00:54 -0800 Subject: [PATCH 05/20] run CI on newer python versions --- .github/workflows/python-package.yml | 2 +- .github/workflows/run-notebooks.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 34af55d8..311dc06c 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -17,7 +17,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10"] + python-version: ["3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v3 diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 0200665b..42b1b263 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -16,7 +16,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.11"] + python-version: ["3.12"] steps: - uses: actions/checkout@v3 From 83695fbf9e1f5e1e6365fab1eb6ec74c47297a37 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 15:01:12 -0800 Subject: [PATCH 06/20] install jupyter in workflow env --- .github/workflows/run-notebooks.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 42b1b263..eade90c6 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -27,6 +27,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip + pip install jupyter if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: Run tutorial notebooks run: | From cd620b3624fe1532fca1a5092aeccab711d4a8af Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 15:05:21 -0800 Subject: [PATCH 07/20] also need to install orbitize in ci env --- .github/workflows/run-notebooks.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index eade90c6..8a6c45c7 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -29,6 +29,7 @@ jobs: python -m pip install --upgrade pip pip install jupyter if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + pip install . - name: Run tutorial notebooks run: | jupyter execute docs/tutorials/*.ipynb From e5c7b6a0bfd3f92fe7c4e0d1a4b88fd2b3559f2f Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 15:17:23 -0800 Subject: [PATCH 08/20] trying to get nbs to run --- .github/workflows/run-notebooks.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 8a6c45c7..dbb974f0 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -27,10 +27,10 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install jupyter - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - pip install . + python -m pip install jupyter + python -m pip install install -r requirements.txt - name: Run tutorial notebooks run: | jupyter execute docs/tutorials/*.ipynb + shell: bash From c34ab4bc376e5d1864201185c4f878e0b11b4a83 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 15:35:30 -0800 Subject: [PATCH 09/20] trying again to get nbs to run --- .github/workflows/run-notebooks.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index dbb974f0..38d7165c 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -28,9 +28,9 @@ jobs: run: | python -m pip install --upgrade pip python -m pip install jupyter - python -m pip install install -r requirements.txt + python -m pip install -r requirements.txt + python -m pip install . - name: Run tutorial notebooks run: | jupyter execute docs/tutorials/*.ipynb - shell: bash From 185fcc21ecc21d8d054b9c120ae8da0e477ea6cc Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 15:47:17 -0800 Subject: [PATCH 10/20] trying again --- .github/workflows/run-notebooks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 38d7165c..dd618e09 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -29,7 +29,7 @@ jobs: python -m pip install --upgrade pip python -m pip install jupyter python -m pip install -r requirements.txt - python -m pip install . + python setup.py install - name: Run tutorial notebooks run: | jupyter execute docs/tutorials/*.ipynb From dae000e550ed280c311d64bc802117073e1cc8c7 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 15:50:17 -0800 Subject: [PATCH 11/20] and again! --- .github/workflows/run-notebooks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index dd618e09..bb8495b5 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -27,7 +27,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install jupyter + python -m pip install jupyter setuptools python -m pip install -r requirements.txt python setup.py install - name: Run tutorial notebooks From 812a823374b5f60b3c9a728c57d00b69c5b47630 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 16:00:02 -0800 Subject: [PATCH 12/20] debugging nb action --- .github/workflows/run-notebooks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index bb8495b5..8b92d7c8 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -29,8 +29,8 @@ jobs: python -m pip install --upgrade pip python -m pip install jupyter setuptools python -m pip install -r requirements.txt - python setup.py install - name: Run tutorial notebooks run: | + echo $PATH jupyter execute docs/tutorials/*.ipynb From 17b04752f105093a3520e1d07dd37ee31c342e23 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 16:02:59 -0800 Subject: [PATCH 13/20] more debugging --- .github/workflows/run-notebooks.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 8b92d7c8..b9e1b626 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -32,5 +32,6 @@ jobs: - name: Run tutorial notebooks run: | echo $PATH + pip list jupyter execute docs/tutorials/*.ipynb From 38c0d31c8a67e1f1ac111069e7b8eff83104c3da Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 16:08:34 -0800 Subject: [PATCH 14/20] more debugging --- .github/workflows/run-notebooks.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index b9e1b626..285c1de4 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -29,6 +29,10 @@ jobs: python -m pip install --upgrade pip python -m pip install jupyter setuptools python -m pip install -r requirements.txt + - name: Install orbitize + run: | + echo ${{ github.workspace }} + python -m pip install ${{ github.workspace }} - name: Run tutorial notebooks run: | echo $PATH From 785a74de1032bbf6445cbcd041600630280673c7 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 16:12:30 -0800 Subject: [PATCH 15/20] debugging --- .github/workflows/run-notebooks.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 285c1de4..1d5fa53c 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -28,11 +28,9 @@ jobs: run: | python -m pip install --upgrade pip python -m pip install jupyter setuptools - python -m pip install -r requirements.txt - name: Install orbitize run: | - echo ${{ github.workspace }} - python -m pip install ${{ github.workspace }} + python -m pip install -r . - name: Run tutorial notebooks run: | echo $PATH From a64a29dc3d0e6abd469d11a3086adcb3d6e23bbe Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 16:19:08 -0800 Subject: [PATCH 16/20] more debugging --- .github/workflows/run-notebooks.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 1d5fa53c..67f66b8b 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -28,9 +28,8 @@ jobs: run: | python -m pip install --upgrade pip python -m pip install jupyter setuptools - - name: Install orbitize - run: | - python -m pip install -r . + python -m pip install -r requirements.txt + python -m pip install . - name: Run tutorial notebooks run: | echo $PATH From a54cbed07798e1a8b766bff815448b2a87fdad64 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 16:25:38 -0800 Subject: [PATCH 17/20] more debugging --- .github/workflows/run-notebooks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 67f66b8b..137d798d 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -29,7 +29,7 @@ jobs: python -m pip install --upgrade pip python -m pip install jupyter setuptools python -m pip install -r requirements.txt - python -m pip install . + python -m pip install . --no-build-isolation - name: Run tutorial notebooks run: | echo $PATH From 4b8acdfe5ee5cb007bdaf7bd648626e53c949744 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 16:29:12 -0800 Subject: [PATCH 18/20] more debugging --- .github/workflows/run-notebooks.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 137d798d..1b850ab2 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -27,8 +27,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install jupyter setuptools - python -m pip install -r requirements.txt + python -m pip install jupyter setuptools --no-build-isolation + python -m pip install -r requirements.txt --no-build-isolation python -m pip install . --no-build-isolation - name: Run tutorial notebooks run: | From 32a430b776579fef9eb459726b036d5a94e30b04 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 16:30:30 -0800 Subject: [PATCH 19/20] new error, making progress --- .github/workflows/run-notebooks.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 1b850ab2..2aa434ad 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -27,8 +27,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - python -m pip install jupyter setuptools --no-build-isolation - python -m pip install -r requirements.txt --no-build-isolation + python -m pip install jupyter setuptools wheel + python -m pip install -r requirements.txt python -m pip install . --no-build-isolation - name: Run tutorial notebooks run: | From 63e468aaf43753c0f9531a67834d0407ea3084a0 Mon Sep 17 00:00:00 2001 From: Sarah Blunt Date: Wed, 10 Jan 2024 16:34:16 -0800 Subject: [PATCH 20/20] success!! remove debugging stmts --- .github/workflows/run-notebooks.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/run-notebooks.yml b/.github/workflows/run-notebooks.yml index 2aa434ad..92a428e8 100644 --- a/.github/workflows/run-notebooks.yml +++ b/.github/workflows/run-notebooks.yml @@ -32,7 +32,5 @@ jobs: python -m pip install . --no-build-isolation - name: Run tutorial notebooks run: | - echo $PATH - pip list jupyter execute docs/tutorials/*.ipynb