From a6142110738ec0bcf5c0d35e5a1feab3c7188b2b Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 13:14:34 -0400 Subject: [PATCH 01/19] Updating gitignore to allow for adding html files --- .gitignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitignore b/.gitignore index 643ae47a6..1b7f3bc16 100644 --- a/.gitignore +++ b/.gitignore @@ -11,7 +11,6 @@ docker/ *.egg *.coverage *.ipynb -*.html *.pickle *.xlsx From cf0fc8bb035930ec89835902acc4495bdbe432cd Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 13:15:55 -0400 Subject: [PATCH 02/19] Adding in html files for new layout and reverting gitignore --- .gitignore | 1 + documentation/_build/html/index.html | 9 +++++++++ documentation/_templates/versions.html | 27 ++++++++++++++++++++++++++ 3 files changed, 37 insertions(+) create mode 100644 documentation/_build/html/index.html create mode 100644 documentation/_templates/versions.html diff --git a/.gitignore b/.gitignore index 1b7f3bc16..643ae47a6 100644 --- a/.gitignore +++ b/.gitignore @@ -11,6 +11,7 @@ docker/ *.egg *.coverage *.ipynb +*.html *.pickle *.xlsx diff --git a/documentation/_build/html/index.html b/documentation/_build/html/index.html new file mode 100644 index 000000000..0f2d23e78 --- /dev/null +++ b/documentation/_build/html/index.html @@ -0,0 +1,9 @@ + + + + Redirecting to master branch + + + + + \ No newline at end of file diff --git a/documentation/_templates/versions.html b/documentation/_templates/versions.html new file mode 100644 index 000000000..476c8d195 --- /dev/null +++ b/documentation/_templates/versions.html @@ -0,0 +1,27 @@ +{%- if current_version %} +
+ + Other Versions + v: {{ current_version.name }} + + +
+ {%- if versions.tags %} +
+
Tags
+ {%- for item in versions.tags %} +
{{ item.name }}
+ {%- endfor %} +
+ {%- endif %} + {%- if versions.branches %} +
+
Branches
+ {%- for item in versions.branches %} +
{{ item.name }}
+ {%- endfor %} +
+ {%- endif %} +
+
+{%- endif %} \ No newline at end of file From cf67d31d1f36b1118becaab4bfb9c09dc52cb4eb Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 13:16:11 -0400 Subject: [PATCH 03/19] adding sphinx multiversion requirement and configuration --- documentation/conf.py | 7 +++++++ requirements.txt | 1 + 2 files changed, 8 insertions(+) diff --git a/documentation/conf.py b/documentation/conf.py index 84fd2bd2a..7cd6722ce 100644 --- a/documentation/conf.py +++ b/documentation/conf.py @@ -40,6 +40,8 @@ 'sphinx.ext.autosummary', 'sphinx.ext.napoleon', 'sphinx.ext.intersphinx', + 'sphinx_multiversion', + 'sphinxcontrib.jquery', ] napoleon_use_rtype = False @@ -51,6 +53,11 @@ autoclass_content = 'both' numfig=True numfig_format = {'figure': 'Figure %s', 'table': 'Table %s', 'code-block': 'Listing %s'} +# Whitelist pattern for tags (set to None to ignore all tags) +smv_tag_whitelist = None +# Whitelist pattern for branches (set to None to ignore all branches) +smv_branch_whitelist = r'^.*$' + # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] diff --git a/requirements.txt b/requirements.txt index 77fd539c5..8e8f1985d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,6 +16,7 @@ rtree; sys_platform == "darwin" or sys_platform == "linux" # Documentation sphinx sphinx_rtd_theme +sphinx-multiversion # Testing pytest From 5992c7d533d547ae0b97e818ced6c8910aae5b62 Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 13:16:23 -0400 Subject: [PATCH 04/19] adding workflow --- .github/workflows/build_deploy_pages.yml | 46 ++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 .github/workflows/build_deploy_pages.yml diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml new file mode 100644 index 000000000..9fa6905ce --- /dev/null +++ b/.github/workflows/build_deploy_pages.yml @@ -0,0 +1,46 @@ +# This is a basic workflow to help you get started with Actions + +name: Build docs and deploy to pages + +on: + push: + branches: [pages] + workflow_dispatch: +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + with: + fetch-depth: 0 + # - name: Install pandoc + # run: sudo apt-get update -y && sudo apt-get install -y pandoc + - uses: actions/setup-python@v2 + with: + python-version: '3.8' + - name: Install package + run: | + pip install . + pip install -r requirements.txt + - name: Build documentation + run: sphinx-multiversion -b html documentation/ documentation/_build/html + - name: Upload artifact + uses: actions/upload-pages-artifact@v1 + with: + path: 'documentation/_build/html' + + deploy: + needs: build + permissions: + pages: write # to deploy to Pages + id-token: write # to verify the deployment originates from an appropriate source + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + steps: + - name: Setup Pages + uses: actions/configure-pages@v3 + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v1 From fe368f2c6f1b877c0bad073b3d720bc749a2c466 Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 13:20:17 -0400 Subject: [PATCH 05/19] Fixing workflow --- .github/workflows/build_deploy_pages.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index 9fa6905ce..b938298ab 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -8,6 +8,7 @@ on: workflow_dispatch: jobs: build: + name: Build the documentation with Sphinx runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 @@ -23,15 +24,17 @@ jobs: pip install . pip install -r requirements.txt - name: Build documentation - run: sphinx-multiversion -b html documentation/ documentation/_build/html + run: sphinx-multiversion documentation/ documentation/_build/html - name: Upload artifact uses: actions/upload-pages-artifact@v1 with: path: 'documentation/_build/html' deploy: + name: Deploy documentation to GitHub Pages needs: build permissions: + contents: read pages: write # to deploy to Pages id-token: write # to verify the deployment originates from an appropriate source environment: From e153a36b23abaf5d81e92bbdc0e37004df815f54 Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 13:39:48 -0400 Subject: [PATCH 06/19] adding -e option for build proc --- .github/workflows/build_deploy_pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index b938298ab..45b9b7706 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -21,7 +21,7 @@ jobs: python-version: '3.8' - name: Install package run: | - pip install . + pip install -e . pip install -r requirements.txt - name: Build documentation run: sphinx-multiversion documentation/ documentation/_build/html From 9c144fffe32a78dd37857ab61e6d4a75f8a62168 Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 14:01:18 -0400 Subject: [PATCH 07/19] trying to fix branch issue --- .github/workflows/build_deploy_pages.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index 45b9b7706..478c4fae1 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -11,9 +11,10 @@ jobs: name: Build the documentation with Sphinx runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 0 + ref: "main" # - name: Install pandoc # run: sudo apt-get update -y && sudo apt-get install -y pandoc - uses: actions/setup-python@v2 From 480d5999ec99d8a97f1dde38ad383a2cd7982c8e Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 15:12:26 -0400 Subject: [PATCH 08/19] troubleshooting --- .github/workflows/build_deploy_pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index 478c4fae1..3993f9955 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -14,9 +14,9 @@ jobs: - uses: actions/checkout@v3 with: fetch-depth: 0 - ref: "main" # - name: Install pandoc # run: sudo apt-get update -y && sudo apt-get install -y pandoc + - run: git branch - uses: actions/setup-python@v2 with: python-version: '3.8' From e0a1915bcb71956fc8af88b7c202c57ca5c8f95f Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 15:12:32 -0400 Subject: [PATCH 09/19] troubleshooting --- .github/workflows/build_deploy_pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index 3993f9955..b3b266dc7 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -4,7 +4,7 @@ name: Build docs and deploy to pages on: push: - branches: [pages] + branches: [main, pages] workflow_dispatch: jobs: build: From 63a21cd7567156321a28d3df11b6050d44c05272 Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 17:53:51 -0400 Subject: [PATCH 10/19] another troubleshooting attempt --- .github/workflows/build_deploy_pages.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index b3b266dc7..68f5f2710 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -14,8 +14,7 @@ jobs: - uses: actions/checkout@v3 with: fetch-depth: 0 - # - name: Install pandoc - # run: sudo apt-get update -y && sudo apt-get install -y pandoc + - run: git fetch --no-tags --depth=1 origin master - run: git branch - uses: actions/setup-python@v2 with: From 092b3977c4ab917172eec65fd780582093baaf78 Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 18:25:16 -0400 Subject: [PATCH 11/19] another attempt --- .github/workflows/build_deploy_pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index 68f5f2710..31bef640e 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -14,7 +14,7 @@ jobs: - uses: actions/checkout@v3 with: fetch-depth: 0 - - run: git fetch --no-tags --depth=1 origin master + - run: git fetch --no-tags --depth=1 origin - run: git branch - uses: actions/setup-python@v2 with: From a72d291103aa10bb252c7d0041f00750ab4c4f62 Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 18:36:09 -0400 Subject: [PATCH 12/19] more troubleshooting --- .github/workflows/build_deploy_pages.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index 31bef640e..a24b327b9 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -15,7 +15,10 @@ jobs: with: fetch-depth: 0 - run: git fetch --no-tags --depth=1 origin - - run: git branch + - name: troubleshooting + run: | + git branch + git remote -v - uses: actions/setup-python@v2 with: python-version: '3.8' From 6101400708fec061a21ccb12d60afe1e7f92498d Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 18:44:43 -0400 Subject: [PATCH 13/19] troubleshooting --- .github/workflows/build_deploy_pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index a24b327b9..b02fc0c39 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -14,7 +14,7 @@ jobs: - uses: actions/checkout@v3 with: fetch-depth: 0 - - run: git fetch --no-tags --depth=1 origin + - run: git fetch origin - name: troubleshooting run: | git branch From 53a30a6ede22c264f807d307be2be4bbc0adb2a9 Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 18:45:04 -0400 Subject: [PATCH 14/19] another try --- .github/workflows/build_deploy_pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index b02fc0c39..8a6211a17 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -11,7 +11,7 @@ jobs: name: Build the documentation with Sphinx runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v2 with: fetch-depth: 0 - run: git fetch origin From e716c7b52dbdab0a7de883d32a963a52c4157c6d Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 18:46:21 -0400 Subject: [PATCH 15/19] anotha --- .github/workflows/build_deploy_pages.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index 8a6211a17..169b7b3c3 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -11,10 +11,10 @@ jobs: name: Build the documentation with Sphinx runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: fetch-depth: 0 - - run: git fetch origin + - run: git fetch origin --all - name: troubleshooting run: | git branch From 2d5cbe9fbd9a8209adc5ba3468b247eadc86dd42 Mon Sep 17 00:00:00 2001 From: kbonney Date: Thu, 20 Jul 2023 19:07:51 -0400 Subject: [PATCH 16/19] this has got to work eventually --- .github/workflows/build_deploy_pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index 169b7b3c3..c3d62d291 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -14,7 +14,7 @@ jobs: - uses: actions/checkout@v3 with: fetch-depth: 0 - - run: git fetch origin --all + - run: git fetch origin main - name: troubleshooting run: | git branch From 88df1fa1ddc1bf3c4265a46981345bbf8da0fa78 Mon Sep 17 00:00:00 2001 From: kbonney Date: Mon, 14 Aug 2023 12:50:00 -0400 Subject: [PATCH 17/19] Removing multiversion code --- documentation/_build/html/index.html | 9 --------- documentation/_templates/versions.html | 27 -------------------------- documentation/conf.py | 7 ------- requirements.txt | 1 - 4 files changed, 44 deletions(-) delete mode 100644 documentation/_build/html/index.html delete mode 100644 documentation/_templates/versions.html diff --git a/documentation/_build/html/index.html b/documentation/_build/html/index.html deleted file mode 100644 index 0f2d23e78..000000000 --- a/documentation/_build/html/index.html +++ /dev/null @@ -1,9 +0,0 @@ - - - - Redirecting to master branch - - - - - \ No newline at end of file diff --git a/documentation/_templates/versions.html b/documentation/_templates/versions.html deleted file mode 100644 index 476c8d195..000000000 --- a/documentation/_templates/versions.html +++ /dev/null @@ -1,27 +0,0 @@ -{%- if current_version %} -
- - Other Versions - v: {{ current_version.name }} - - -
- {%- if versions.tags %} -
-
Tags
- {%- for item in versions.tags %} -
{{ item.name }}
- {%- endfor %} -
- {%- endif %} - {%- if versions.branches %} -
-
Branches
- {%- for item in versions.branches %} -
{{ item.name }}
- {%- endfor %} -
- {%- endif %} -
-
-{%- endif %} \ No newline at end of file diff --git a/documentation/conf.py b/documentation/conf.py index 7cd6722ce..84fd2bd2a 100644 --- a/documentation/conf.py +++ b/documentation/conf.py @@ -40,8 +40,6 @@ 'sphinx.ext.autosummary', 'sphinx.ext.napoleon', 'sphinx.ext.intersphinx', - 'sphinx_multiversion', - 'sphinxcontrib.jquery', ] napoleon_use_rtype = False @@ -53,11 +51,6 @@ autoclass_content = 'both' numfig=True numfig_format = {'figure': 'Figure %s', 'table': 'Table %s', 'code-block': 'Listing %s'} -# Whitelist pattern for tags (set to None to ignore all tags) -smv_tag_whitelist = None -# Whitelist pattern for branches (set to None to ignore all branches) -smv_branch_whitelist = r'^.*$' - # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] diff --git a/requirements.txt b/requirements.txt index 8e8f1985d..77fd539c5 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,7 +16,6 @@ rtree; sys_platform == "darwin" or sys_platform == "linux" # Documentation sphinx sphinx_rtd_theme -sphinx-multiversion # Testing pytest From e5032d736c6b0b15cacd890de29e827155378109 Mon Sep 17 00:00:00 2001 From: kbonney Date: Mon, 14 Aug 2023 12:53:46 -0400 Subject: [PATCH 18/19] Removing sphinx-multiversion command --- .github/workflows/build_deploy_pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index c3d62d291..05db10bb8 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -27,7 +27,7 @@ jobs: pip install -e . pip install -r requirements.txt - name: Build documentation - run: sphinx-multiversion documentation/ documentation/_build/html + run: sphinx-build documentation/ documentation/_build/html - name: Upload artifact uses: actions/upload-pages-artifact@v1 with: From a244619e18a3d9644e5a77d4aaf36db96287d230 Mon Sep 17 00:00:00 2001 From: kbonney Date: Fri, 18 Aug 2023 09:09:33 -0400 Subject: [PATCH 19/19] removing pages branch from on option --- .github/workflows/build_deploy_pages.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_deploy_pages.yml b/.github/workflows/build_deploy_pages.yml index 05db10bb8..a6eff5624 100644 --- a/.github/workflows/build_deploy_pages.yml +++ b/.github/workflows/build_deploy_pages.yml @@ -4,7 +4,7 @@ name: Build docs and deploy to pages on: push: - branches: [main, pages] + branches: [main] workflow_dispatch: jobs: build: