From be76f834d74e0da2b940b6e9b9992edb0a2e2562 Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Thu, 1 Feb 2024 12:52:11 -0500 Subject: [PATCH 01/15] Update .gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index a8ede0d3d..810d9c1f6 100644 --- a/.gitignore +++ b/.gitignore @@ -81,6 +81,7 @@ target/ # IPython profile_default/ ipython_config.py +Untitled*.ipynb # pyenv .python-version From 902f004c2cce260c7731aaaf6b24cc5d084cc52f Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Thu, 1 Feb 2024 13:02:54 -0500 Subject: [PATCH 02/15] Run nbclean --- docs/notebooks/data_analysis/Remove_lightleak.ipynb | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/docs/notebooks/data_analysis/Remove_lightleak.ipynb b/docs/notebooks/data_analysis/Remove_lightleak.ipynb index c1b2e2c4f..b932e5dab 100644 --- a/docs/notebooks/data_analysis/Remove_lightleak.ipynb +++ b/docs/notebooks/data_analysis/Remove_lightleak.ipynb @@ -131,14 +131,6 @@ "fig.subplots_adjust(wspace=0.5)\n", "plt.show()" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "eda9e234", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { @@ -157,7 +149,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.0" + "version": "3.12.1" } }, "nbformat": 4, From 59fff86a4f261a3415967162de120cd59a6c38fe Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 17:19:48 -0500 Subject: [PATCH 03/15] Remove empty cell at end of notebook --- .../data_analysis/Deconvolving_XRT_images.ipynb | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/docs/notebooks/data_analysis/Deconvolving_XRT_images.ipynb b/docs/notebooks/data_analysis/Deconvolving_XRT_images.ipynb index d9c2139e8..462c47115 100644 --- a/docs/notebooks/data_analysis/Deconvolving_XRT_images.ipynb +++ b/docs/notebooks/data_analysis/Deconvolving_XRT_images.ipynb @@ -98,14 +98,6 @@ "fig.subplots_adjust(wspace=0.5)\n", "plt.show()" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "549d08ea", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { @@ -124,7 +116,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.0" + "version": "3.12.1" } }, "nbformat": 4, From cc81d9edf41094aa443112e8bac633df2219fe10 Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 17:20:20 -0500 Subject: [PATCH 04/15] Rename notebook without underscore --- docs/notebooks/data_analysis/Remove_lightleak.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/notebooks/data_analysis/Remove_lightleak.ipynb b/docs/notebooks/data_analysis/Remove_lightleak.ipynb index b932e5dab..b1499575e 100644 --- a/docs/notebooks/data_analysis/Remove_lightleak.ipynb +++ b/docs/notebooks/data_analysis/Remove_lightleak.ipynb @@ -5,7 +5,7 @@ "id": "075bbcc4", "metadata": {}, "source": [ - "# Using the remove_lightleak function to analyze XRT composite images" + "# Remove lightleaks to analyze XRT composite images" ] }, { From a6e4269dcc7be9923a6a85db52b3c3906e5e6e2a Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 17:41:36 -0500 Subject: [PATCH 05/15] Update GitHub Action to install pandoc from repo --- .github/workflows/testing.yml | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index bac1b43e9..7d074e0df 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -71,7 +71,7 @@ jobs: include: - name: Documentation - python: '3.10' + python: '3.12' steps: @@ -88,8 +88,19 @@ jobs: - name: Install nox run: python -m pip install --progress-bar off --upgrade nox - - name: Install graphviz and pandoc - run: sudo apt install graphviz pandoc + - name: Install graphviz + run: sudo apt install graphviz + + - name: Install pandoc + run: | + # Specify the desired version of Pandoc + PANDOC_VERSION="3.1.11.1" # Update this to the version you need + # Download the pre-built binary package for Linux + wget https://github.com/jgm/pandoc/releases/download/${PANDOC_VERSION}/pandoc-${PANDOC_VERSION}-1-amd64.deb + # Install the downloaded package + sudo dpkg -i pandoc-${PANDOC_VERSION}-1-amd64.deb + # Remove the downloaded package file + rm pandoc-${PANDOC_VERSION}-1-amd64.deb - name: Build documentation run: nox -e build_docs_nitpicky -- -q From e87ac93f1c0435b3786e156eaa66a051506d3d38 Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 17:49:08 -0500 Subject: [PATCH 06/15] Make GitHub Action more concise --- .github/workflows/testing.yml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 7d074e0df..65b9f880d 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -93,14 +93,11 @@ jobs: - name: Install pandoc run: | - # Specify the desired version of Pandoc - PANDOC_VERSION="3.1.11.1" # Update this to the version you need - # Download the pre-built binary package for Linux - wget https://github.com/jgm/pandoc/releases/download/${PANDOC_VERSION}/pandoc-${PANDOC_VERSION}-1-amd64.deb - # Install the downloaded package + PANDOC_VERSION="3.1.11.1" + wget -q https://github.com/jgm/pandoc/releases/download/${PANDOC_VERSION}/pandoc-${PANDOC_VERSION}-1-amd64.deb sudo dpkg -i pandoc-${PANDOC_VERSION}-1-amd64.deb - # Remove the downloaded package file rm pandoc-${PANDOC_VERSION}-1-amd64.deb + pandoc --version - name: Build documentation run: nox -e build_docs_nitpicky -- -q From 25180efc3fdb44b5d6774cc05793654011b74f70 Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 17:57:02 -0500 Subject: [PATCH 07/15] Set upper limit on nbconvert --- requirements/docs.txt | 1 + setup.cfg | 1 + 2 files changed, 2 insertions(+) diff --git a/requirements/docs.txt b/requirements/docs.txt index b09698519..67a0d56a6 100644 --- a/requirements/docs.txt +++ b/requirements/docs.txt @@ -8,6 +8,7 @@ docutils >= 0.18 ipykernel ipython jinja2 != 3.1 +nbconvert < 7.14 nbsphinx >= 0.9 numpydoc >= 1.2 pillow diff --git a/setup.cfg b/setup.cfg index 99de2bd55..daa840cb2 100644 --- a/setup.cfg +++ b/setup.cfg @@ -64,6 +64,7 @@ docs = ipykernel ipython jinja2 != 3.1 + nbconvert < 7.14 nbsphinx >= 0.9 numpydoc >= 1.2 pillow From efeb594300a3418f0fa498d96fa6ae0e6b75a3f0 Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 18:01:56 -0500 Subject: [PATCH 08/15] Revert some changes ...while adding some backticks --- docs/notebooks/data_analysis/Deconvolving_XRT_images.ipynb | 2 +- docs/notebooks/data_analysis/Remove_lightleak.ipynb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/notebooks/data_analysis/Deconvolving_XRT_images.ipynb b/docs/notebooks/data_analysis/Deconvolving_XRT_images.ipynb index 462c47115..d7616c6ec 100644 --- a/docs/notebooks/data_analysis/Deconvolving_XRT_images.ipynb +++ b/docs/notebooks/data_analysis/Deconvolving_XRT_images.ipynb @@ -116,7 +116,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.11.0" } }, "nbformat": 4, diff --git a/docs/notebooks/data_analysis/Remove_lightleak.ipynb b/docs/notebooks/data_analysis/Remove_lightleak.ipynb index b1499575e..600493233 100644 --- a/docs/notebooks/data_analysis/Remove_lightleak.ipynb +++ b/docs/notebooks/data_analysis/Remove_lightleak.ipynb @@ -5,7 +5,7 @@ "id": "075bbcc4", "metadata": {}, "source": [ - "# Remove lightleaks to analyze XRT composite images" + "# Using the `remove_lightleak` function to analyze XRT composite images" ] }, { From cb7a2d0a2e684d735161aaba21cf6c78a5ef9227 Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 18:02:24 -0500 Subject: [PATCH 09/15] Revert a change --- docs/notebooks/data_analysis/Remove_lightleak.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/notebooks/data_analysis/Remove_lightleak.ipynb b/docs/notebooks/data_analysis/Remove_lightleak.ipynb index 600493233..8c76c79e3 100644 --- a/docs/notebooks/data_analysis/Remove_lightleak.ipynb +++ b/docs/notebooks/data_analysis/Remove_lightleak.ipynb @@ -149,7 +149,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.11.0" } }, "nbformat": 4, From 0e2ce80236eb746338b101595f50d99332af39de Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 18:06:53 -0500 Subject: [PATCH 10/15] Remove upper limit on nbconvert --- requirements/docs.txt | 2 +- setup.cfg | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements/docs.txt b/requirements/docs.txt index 67a0d56a6..0214c840e 100644 --- a/requirements/docs.txt +++ b/requirements/docs.txt @@ -8,7 +8,7 @@ docutils >= 0.18 ipykernel ipython jinja2 != 3.1 -nbconvert < 7.14 +nbconvert nbsphinx >= 0.9 numpydoc >= 1.2 pillow diff --git a/setup.cfg b/setup.cfg index daa840cb2..4482ae97f 100644 --- a/setup.cfg +++ b/setup.cfg @@ -64,7 +64,7 @@ docs = ipykernel ipython jinja2 != 3.1 - nbconvert < 7.14 + nbconvert nbsphinx >= 0.9 numpydoc >= 1.2 pillow From 632ed78f36fb1abc1a4dec74993aab2266620989 Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 18:07:29 -0500 Subject: [PATCH 11/15] Build docs on macOS rather than Ubuntu --- .github/workflows/testing.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 65b9f880d..43cb6b7de 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -62,7 +62,7 @@ jobs: documentation: name: ${{ matrix.name }} - runs-on: ubuntu-latest + runs-on: macos-latest strategy: fail-fast: false From b72ac708eed75408a3625c78322e9f88c5105539 Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 18:11:11 -0500 Subject: [PATCH 12/15] Use brew to install graphviz & pandoc --- .github/workflows/testing.yml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 43cb6b7de..38723a7fd 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -89,15 +89,10 @@ jobs: run: python -m pip install --progress-bar off --upgrade nox - name: Install graphviz - run: sudo apt install graphviz + run: brew install graphviz - name: Install pandoc - run: | - PANDOC_VERSION="3.1.11.1" - wget -q https://github.com/jgm/pandoc/releases/download/${PANDOC_VERSION}/pandoc-${PANDOC_VERSION}-1-amd64.deb - sudo dpkg -i pandoc-${PANDOC_VERSION}-1-amd64.deb - rm pandoc-${PANDOC_VERSION}-1-amd64.deb - pandoc --version + run: brew install pandoc - name: Build documentation run: nox -e build_docs_nitpicky -- -q From c058ec6be0ff5e272bfe2d6029bdca6c69a96c4f Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 18:27:49 -0500 Subject: [PATCH 13/15] Revert "Use brew to install graphviz & pandoc" This reverts commit b72ac708eed75408a3625c78322e9f88c5105539. --- .github/workflows/testing.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 38723a7fd..43cb6b7de 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -89,10 +89,15 @@ jobs: run: python -m pip install --progress-bar off --upgrade nox - name: Install graphviz - run: brew install graphviz + run: sudo apt install graphviz - name: Install pandoc - run: brew install pandoc + run: | + PANDOC_VERSION="3.1.11.1" + wget -q https://github.com/jgm/pandoc/releases/download/${PANDOC_VERSION}/pandoc-${PANDOC_VERSION}-1-amd64.deb + sudo dpkg -i pandoc-${PANDOC_VERSION}-1-amd64.deb + rm pandoc-${PANDOC_VERSION}-1-amd64.deb + pandoc --version - name: Build documentation run: nox -e build_docs_nitpicky -- -q From 514858d5dafe03e0e64625bcc76007ab54d0512f Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 18:27:54 -0500 Subject: [PATCH 14/15] Revert "Build docs on macOS rather than Ubuntu" This reverts commit 632ed78f36fb1abc1a4dec74993aab2266620989. --- .github/workflows/testing.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 43cb6b7de..65b9f880d 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -62,7 +62,7 @@ jobs: documentation: name: ${{ matrix.name }} - runs-on: macos-latest + runs-on: ubuntu-latest strategy: fail-fast: false From b688c16c0f5a69ca72c98b0f4de79f8d30d7e6e3 Mon Sep 17 00:00:00 2001 From: Nick Murphy Date: Fri, 2 Feb 2024 18:27:56 -0500 Subject: [PATCH 15/15] Revert "Remove upper limit on nbconvert" This reverts commit 0e2ce80236eb746338b101595f50d99332af39de. --- requirements/docs.txt | 2 +- setup.cfg | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements/docs.txt b/requirements/docs.txt index 0214c840e..67a0d56a6 100644 --- a/requirements/docs.txt +++ b/requirements/docs.txt @@ -8,7 +8,7 @@ docutils >= 0.18 ipykernel ipython jinja2 != 3.1 -nbconvert +nbconvert < 7.14 nbsphinx >= 0.9 numpydoc >= 1.2 pillow diff --git a/setup.cfg b/setup.cfg index 4482ae97f..daa840cb2 100644 --- a/setup.cfg +++ b/setup.cfg @@ -64,7 +64,7 @@ docs = ipykernel ipython jinja2 != 3.1 - nbconvert + nbconvert < 7.14 nbsphinx >= 0.9 numpydoc >= 1.2 pillow