fixed import error in docs workflow (#35)

* fixed import error; added paste2 into the documentation as well

.github/workflows/docs.yml

@@ -22,10 +22,17 @@ jobs:
 
       - name: Install Python dependencies
         run: |
-          pip install sphinx myst-parser sphinx-autodoc-typehints nbsphinx sphinx-gallery sphinx-rtd-theme
+          pip install sphinx myst-parser sphinx-autodoc-typehints nbsphinx sphinx-gallery sphinx-rtd-theme sphinx-autodoc-annotation
 
       - uses: actions/checkout@v2
 
+      - name: Install Package
+        run: | 
+         pip install . 
+
+      - name: Install Pandoc
+        run: sudo apt-get install -y pandoc
+
       - name: Setup Envvars
         run: |
             if [[ $GITHUB_REF = "refs/tags/"* ]] ; then echo "PASTE3_VERSION=${GITHUB_REF/refs\/tags\//}" ; else echo "PASTE3_VERSION=" ; fi >> $GITHUB_ENV
@@ -34,10 +41,10 @@ jobs:
         run: |
           # Unless we add a .nojekyll to the base of the deployment folder, the underscores in foldernames
           # like _static/ etc. pose problems on GH Pages.
-          cd docs && sphinx-apidoc -f -o src ../src/paste -H Modules && make html && touch _build/html/.nojekyll
+          cd docs && sphinx-apidoc -f -o src ../src/paste3 -H Modules && make html && touch build/html/.nojekyll
 
       - name: Deploy
         uses: JamesIves/github-pages-deploy-action@v4
         with:
-          folder: docs/_build/html
+          folder: docs/build/html
           branch: gh-pages

docs/make.bat

@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.https://www.sphinx-doc.org/
-	exit /b 1
-)
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/paste3/installation.md

@@ -0,0 +1,28 @@
+# Setting up the environment 
+
+1. Clone the repository and enter it: 
+```shell
+  git clone [email protected]:raphael-group/paste3.git
+  cd paste3
+```
+2. Create and activate a conda environment using the provided `environment.yml` file: 
+```shell
+   conda env create --file environment.yml
+   conda activate paste
+```
+The command prompt will change to indicate the new conda environment by prepending `(paste)`. 
+3. When you are done using the package, deactivate the `paste` environment and return to `(base)` by entering the following command: 
+```shell
+conda deactivate
+```
+
+# Installation 
+
+1. Enter the `paste3` repository cloned before setting up the environment
+```shell
+cd paste3
+```
+2. Install the package:
+```shell
+pip install . 
+```

docs/source/api.rst

@@ -1,22 +1,28 @@
 API
 ===
+    import paste3
+.. automodule:: paste3
 
-Import Paste as::
+PASTE Alignment
+~~~~~~~~~~~~~~~~~~
 
-   from paste.visualization import plot_slice, stack_slices_pairwise, stack_slices_center
-   from paste.paste import pairwise_align, center_align
-   from paste.helper import filter_for_common_genes, match_spots_using_spatial_heuristic, match_spots_using_spatial_heuristic, apply_trsf
+.. autosummary::
+   :toctree: api
 
-.. automodule:: paste
+    paste.pairwise_align
+    paste.center_align
 
-Alignment
-~~~~~~~~~
+PASTE2 Alignment
+~~~~~~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: api
 
-    PASTE.pairwise_align
-    PASTE.center_align
+    paste2.partial_pairwise_align_given_cost_matrix
+    paste2.partial_pairwise_align_histology
+    paste2.partial_pairwise_align
+    paste2.partial_fused_gromov_wasserstein
+    paste2.gwgrad_partial
 
 Visualization
 ~~~~~~~~~~~~~
@@ -28,6 +34,42 @@ Visualization
     visualization.stack_slices_center
     visualization.plot_slice
 
+Projection
+~~~~~~~~~~~~~
+
+.. autosummary::
+   :toctree: api
+
+    projection.partial_stack_slices_pairwise
+    projection.partial_procrustes_analysis
+
+Model Selection
+~~~~~~~~~~~~~~~~
+
+.. autosummary::
+   :toctree: api
+
+    model_selection.create_graph
+    model_selection.generate_graph_from_labels
+    model_selection.edge_inconsistency_score
+    model_selection.calculate_convex_hull_edge_inconsistency
+    model_selection.plot_edge_curve
+    model_selection.select_overlap_fraction_plotting
+
+
+GLMPCA
+~~~~~~~
+
+.. autosummary::
+   :toctree: api
+
+    glmpca.ortho
+    glmpca.mat_binom_dev
+    glmpca.glmpca_init
+    glmpca.est_nb_theta
+    glmpca.glmpca
+
+
 Miscellaneous
 ~~~~~~~~~~~~~
 
@@ -36,6 +78,4 @@ Miscellaneous
 
    helper.filter_for_common_genes
    helper.match_spots_using_spatial_heuristic
-   helper.apply_trsf
-
 

docs/source/conf.py

@@ -1,24 +1,16 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
 from pathlib import Path
-
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-
 import sys
+import os
 HERE = Path(__file__).parent
-sys.path.insert(0, str(HERE.parent.parent) + '/src') 
+sys.path.insert(0, os.path.abspath(HERE.parent.parent))
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 # -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = 'paste3'
 copyright = '2022, Raphael Lab'
@@ -27,15 +19,12 @@
 # The full version, including alpha/beta/rc tags
 release = '1.2.0'
 
-
 # -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
 extensions = [
     "myst_parser",
-    'sphinx.ext.autosummary', 
+    'sphinx.ext.autosummary',
     "sphinx.ext.autodoc",
     'sphinx.ext.napoleon',
     "sphinx_autodoc_typehints",
@@ -44,41 +33,13 @@
     "sphinx.ext.viewcode"
 ]
 
-# Moves Type hints from function header into description
-autodoc_typehints = "description"
-
-
-# Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = []
 
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-add_module_names = False
-
-
+language = 'python'
 
 # -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'sphinx_rtd_theme'
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
+html_theme = "sphinx_rtd_theme"
 html_static_path = ['_static']
-
-html_show_sourcelink = False
-html_show_sphinx = False
-
-
-
-nbsphinx_thumbnails = {
-    "notebooks/getting-started": "_static/images/breast_stack_2d.png",
-}