Expand tests (#22)

* Added simulation framework tests. * Add initialization test. * Update `README` to better reflect current dev workflow. Also make some formatting improvements. * Added multigroup test for spatial affinity groups. * Remove deprecated arguments in `load_anndata`. Also reformat `io.py`. * Add linter configurations to `pyproject.toml`. * Fix import name for `test_util.py`. * Add configuration for pre-commit. * Update test data. * Fix analysis tests. Fix analysis functions to match new tests. Fix code style. * Add tests for and refactor `simulation_framework.py`. * Finish `MultiReplicateSyntheticDataset` tests. Refactor accordingly. Add test data/expected outputs. * Fixes to `_canvas.py` and `simulation_framework.py`. * Add documentation for simulations. Fix intiialization tests. * Fix up binning test. Also update dependencies to use compatible versions of newest `squidpy` and `anndata`. See `https://github.com/scverse/squidpy/pull/891`.
alam-shahul · Sep 23, 2024 · cf49313 · cf49313
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,49 @@
+repos:
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+        args: [-c=.yamllint.yml]
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+
+  - repo: https://github.com/asottile/add-trailing-comma
+    rev: v3.1.0
+    hooks:
+      - id: add-trailing-comma
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.16.0
+    hooks:
+      - id: pyupgrade
+
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+        args: ["--safe"]
+
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.5
+    hooks:
+      - id: docformatter
+        name: Format docstring
+        args: [--in-place, --wrap-summaries, "80", --wrap-descriptions, "80", --blank]
+
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.17
+    hooks:
+      - id: mdformat
+        name: Format markdown
+        additional_dependencies:
+          - mdformat-gfm
diff --git a/README.md b/README.md
@@ -1,6 +1,5 @@
 # Popari
 
-
 Popari is a versatile framework for joint analysis and investigation of complex spatial transcriptomics datasets. Read the documentation (including installation instructions) [here](https://popari.readthedocs.io/en/latest/).
 
 > :warning: **Popari is still under active development.** Check back in a bit for a more complete user experience!
@@ -9,14 +8,12 @@ Popari is a versatile framework for joint analysis and investigation of complex
   <img src="./popari_overview_v5.png" width="800">
 </p>
 
-## Dev Instructions
-### Install
+## Dev instructions
 
-```
-pip install popari
-```
+For development, create a fresh Python environment; this should not contain the PyPI-published
+version of the package.
 
-### Publishing
+### PyPI publishing
 
 ```
 pip install hatch
@@ -25,41 +22,53 @@ pip install keyrings.alt
 hatch build
 hatch publish
 ```
+
 Username: `__token__`
 Password: `{API token for PyPI}`
 
-### Tests
+### Running `pytest` tests
 
-To run the provided tests and ensure that SpiceMix can run on your platform, follow the instructions below:
+To run the provided tests and ensure that Popari can run on your platform, follow the instructions below:
 
-- Download this repo.
-```console
-git clone https://github.com/alam-shahul/SpiceMixPlus.git
-```
 - Install `pytest` in your environment.
+
 ```console
 pip install pytest
 ```
-- Navigate to the root directory of this repo.
-- Run the following command. With GPU resources, this test should execute without errors in ~2.5 minutes:
+
+- Navigate to the root directory of this repo, and run all tests with
+
+```console
+python -m pytest -s
+```
+
+- Alternatively, run a single test suite as below:
+
 ```console
 python -m pytest -s tests/test_popari_shared.py
 ```
+
 ### Building Documentation
 
 Assuming you have CMake:
 
 1. Navigate to `docs/`.
+
 ```console
 cd docs/
 ```
+
 2. Install Sphinx requirements.
+
 ```console
 pip install -r requirements.txt
 ```
+
 3. Clean and build.
+
 ```console
 make clean
 make html
 ```
+
 4. Push to GitHub, and documentation will automatically build.
diff --git a/docs/source/api.md b/docs/source/api.md
@@ -26,7 +26,7 @@ Tools for loading and saving Popari data and parameters.
 .. autosummary::
     :toctree: api/
     :recursive:
-    
+
     io.save_anndata
     io.load_anndata
 ```
@@ -42,7 +42,7 @@ Entry points for implementations of the Popari algorithm.
 .. autosummary::
     :toctree: api/
     :recursive:
-    
+
     model.Popari
     model.load_trained_model
 ```
@@ -58,7 +58,7 @@ Objects that are helpful for working with Popari.
 .. autosummary::
     :toctree: api/
     :recursive:
-    
+
     components.PopariDataset
 ```
 
@@ -73,7 +73,7 @@ Functions for visualizing and evaluating Popari results.
 .. autosummary::
     :toctree: api/
     :recursive:
- 
+
     tl.preprocess_embeddings
     tl.leiden
     tl.compute_ari_scores
@@ -98,11 +98,28 @@ Functions for visualizing and evaluating Popari results.
 .. autosummary::
     :toctree: api/
     :recursive:
- 
+
     pl.in_situ
     pl.all_embeddings
     pl.metagene_embedding
     pl.multireplicate_heatmap
     pl.multigroup_heatmap
     pl.confusion_matrix
 ```
+
+## Simulation
+
+Tools to generate simulated (multisample) spatially-resolved transcriptomics, or (m)SRT.
+
+```{eval-rst}
+.. module:: popari.simulation_framework
+.. currentmodule:: popari
+
+.. autosummary::
+    :toctree: api/
+    :recursive:
+
+    simulation_framework.SimulationParameters
+    simulation_framework.SyntheticDataset
+    simulation_framework.MultiReplicateSyntheticDataset
+```
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -12,17 +12,18 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'popari'
-copyright = 'Ma Lab @ CMU, 2022'
-author = 'Shahul Alam'
+project = "popari"
+copyright = "Ma Lab @ CMU, 2024"
+author = "Shahul Alam"
 
 # The full version, including alpha/beta/rc tags
-release = '0.0.1'
+release = "0.0.1"
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,21 +32,21 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autosummary',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autodoc.typehints',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'myst_nb',
-    'sphinx_copybutton',
-    'sphinx_remove_toctrees'
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autodoc.typehints",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "myst_nb",
+    "sphinx_copybutton",
+    "sphinx_remove_toctrees",
 ]
 
 # filetypes to use for documentation
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -58,16 +59,16 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_book_theme'
+html_theme = "sphinx_book_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_static_path = ['_static']
+html_static_path = ["_static"]
 
 # -- Options for included extensions -----------------------------------------
 
-autosummary_generate=True
+autosummary_generate = True
 # nbsphinx_execute = 'never'
 # nbsphinx_allow_directives = True
 nb_execution_mode = "off"
@@ -80,4 +81,3 @@
     "repository_url": "https://github.com/alam-shahul/popari",
     "use_repository_button": True,
 }
-