Update doc files and set up docu workflow to deploy sphinx to gh page…

…s. (#769)
icecube · Apr 26, 2024 · 41f5790 · 41f5790
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diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -0,0 +1,33 @@
+# This workflow will install Python dependencies, produce the sphinx documentation, and publish it to GitHub pages
+
+name: documentation
+
+on:
+  push:
+    branches:
+      - 'master'
+    tags:
+      - '*'
+
+jobs:
+  documentation:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v1
+      with:
+        python-version: '3.10'
+    - name: Install dependencies
+      run: |
+        python -m pip install "pip<21.3"
+        pip install .[develop]
+    - name: Build the docs
+      run: |
+        sphinx-apidoc -f -o docs/source pisa
+        cd docs && make html
+    - name: Deploy to gh pages
+      uses: peaceiris/actions-gh-pages@v3.9.2
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html
diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 
 [Introduction](pisa/README.md) |
 [Installation](INSTALL.md) |
-[Documentation](http://icecube.wisc.edu/%7Epeller/pisa_docs/index.html) |
+[Documentation](https://icecube.github.io/pisa/) |
 [Terminology](pisa/glossary.md) |
 [License](LICENSE) |
 [Contributors](CONTRIBUTORS.md) |

diff --git a/docs/source/pisa.stages.aeff.rst b/docs/source/pisa.stages.aeff.rst
@@ -20,6 +20,14 @@ pisa.stages.aeff.weight module
    :undoc-members:
    :show-inheritance:
 
+pisa.stages.aeff.weight\_hnl module
+-----------------------------------
+
+.. automodule:: pisa.stages.aeff.weight_hnl
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Module contents
 ---------------
 

diff --git a/docs/source/pisa.stages.data.rst b/docs/source/pisa.stages.data.rst
@@ -44,6 +44,22 @@ pisa.stages.data.grid module
    :undoc-members:
    :show-inheritance:
 
+pisa.stages.data.licloader\_weighter module
+-------------------------------------------
+
+.. automodule:: pisa.stages.data.licloader_weighter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pisa.stages.data.meows\_loader module
+-------------------------------------
+
+.. automodule:: pisa.stages.data.meows_loader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pisa.stages.data.simple\_data\_loader module
 --------------------------------------------
 
@@ -60,6 +76,14 @@ pisa.stages.data.simple\_signal module
    :undoc-members:
    :show-inheritance:
 
+pisa.stages.data.sqlite\_loader module
+--------------------------------------
+
+.. automodule:: pisa.stages.data.sqlite_loader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pisa.stages.data.toy\_event\_generator module
 ---------------------------------------------
 

diff --git a/docs/source/pisa.stages.discr_sys.rst b/docs/source/pisa.stages.discr_sys.rst
@@ -12,6 +12,14 @@ pisa.stages.discr\_sys.hypersurfaces module
    :undoc-members:
    :show-inheritance:
 
+pisa.stages.discr\_sys.ultrasurfaces module
+-------------------------------------------
+
+.. automodule:: pisa.stages.discr_sys.ultrasurfaces
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Module contents
 ---------------
 

diff --git a/docs/source/pisa.stages.flux.rst b/docs/source/pisa.stages.flux.rst
@@ -4,6 +4,22 @@ pisa.stages.flux package
 Submodules
 ----------
 
+pisa.stages.flux.airs module
+----------------------------
+
+.. automodule:: pisa.stages.flux.airs
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pisa.stages.flux.astrophysical module
+-------------------------------------
+
+.. automodule:: pisa.stages.flux.astrophysical
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pisa.stages.flux.barr\_simple module
 ------------------------------------
 
@@ -12,6 +28,22 @@ pisa.stages.flux.barr\_simple module
    :undoc-members:
    :show-inheritance:
 
+pisa.stages.flux.daemon\_flux module
+------------------------------------
+
+.. automodule:: pisa.stages.flux.daemon_flux
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+pisa.stages.flux.hillasg module
+-------------------------------
+
+.. automodule:: pisa.stages.flux.hillasg
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pisa.stages.flux.honda\_ip module
 ---------------------------------
 

diff --git a/docs/source/pisa.stages.osc.rst b/docs/source/pisa.stages.osc.rst
@@ -12,6 +12,14 @@ Subpackages
 Submodules
 ----------
 
+pisa.stages.osc.decay\_params module
+------------------------------------
+
+.. automodule:: pisa.stages.osc.decay_params
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pisa.stages.osc.decoherence module
 ----------------------------------
 
@@ -36,6 +44,14 @@ pisa.stages.osc.layers module
    :undoc-members:
    :show-inheritance:
 
+pisa.stages.osc.lri\_params module
+----------------------------------
+
+.. automodule:: pisa.stages.osc.lri_params
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pisa.stages.osc.nsi\_params module
 ----------------------------------
 
@@ -68,6 +84,14 @@ pisa.stages.osc.prob3 module
    :undoc-members:
    :show-inheritance:
 
+pisa.stages.osc.scaling\_params module
+--------------------------------------
+
+.. automodule:: pisa.stages.osc.scaling_params
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pisa.stages.osc.two\_nu\_osc module
 -----------------------------------
 

diff --git a/docs/source/pisa.stages.rst b/docs/source/pisa.stages.rst
@@ -20,17 +20,6 @@ Subpackages
    pisa.stages.utils
    pisa.stages.xsec
 
-Submodules
-----------
-
-pisa.stages.empty\_stage module
--------------------------------
-
-.. automodule:: pisa.stages.empty_stage
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 Module contents
 ---------------
 

diff --git a/docs/source/pisa.stages.utils.rst b/docs/source/pisa.stages.utils.rst
@@ -20,6 +20,14 @@ pisa.stages.utils.adhoc\_sys module
    :undoc-members:
    :show-inheritance:
 
+pisa.stages.utils.bootstrap module
+----------------------------------
+
+.. automodule:: pisa.stages.utils.bootstrap
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pisa.stages.utils.fix\_error module
 -----------------------------------
 

diff --git a/docs/source/pisa.utils.llh_defs.rst b/docs/source/pisa.utils.llh_defs.rst
@@ -15,22 +15,6 @@ pisa.utils.llh\_defs.poisson module
 pisa.utils.llh\_defs.poisson\_gamma\_mixtures module
 ----------------------------------------------------
 
-.. automodule:: pisa.utils.llh_defs.poisson_gamma_mixtures
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-pisa.utils.llh\_defs.poisson\_gamma\_mixtures module
-----------------------------------------------------
-
-.. automodule:: pisa.utils.llh_defs.poisson_gamma_mixtures
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-pisa.utils.llh\_defs.poisson\_gamma\_mixtures module
-----------------------------------------------------
-
 .. automodule:: pisa.utils.llh_defs.poisson_gamma_mixtures
    :members:
    :undoc-members:

diff --git a/docs/source/pisa.utils.rst b/docs/source/pisa.utils.rst
@@ -29,6 +29,14 @@ pisa.utils.barr\_parameterization module
    :undoc-members:
    :show-inheritance:
 
+pisa.utils.callable module
+--------------------------
+
+.. automodule:: pisa.utils.callable
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 pisa.utils.comparisons module
 -----------------------------
 

diff --git a/pisa_examples/README.ipynb b/pisa_examples/README.ipynb