Merge pull request #135 from vineetbansal/develop

Testing/CI/Versioning

.github/workflows/docs.yml

@@ -0,0 +1,39 @@
+name: Docs 
+
+on:
+  push:
+    branches: [ master, develop, docs ]
+    tags:
+      - '*'
+
+jobs:
+
+  build_docs:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: [3.9]
+
+    steps:
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install Python dependencies
+        run: |
+          pip install sphinx myst-parser sphinx-book-theme
+
+      - uses: actions/checkout@v2
+
+      - name: Build docs
+        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 && make html && touch _build/html/.nojekyll
+
+      - name: Deploy
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: docs/_build/html
+          branch: gh-pages

.github/workflows/main.yml

@@ -0,0 +1,37 @@
+name: CI
+
+on:
+  push:
+    branches: [ master, develop ]
+  pull_request:
+    branches: [ master, develop ]
+
+jobs:
+  run_tests:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: [3.7, 3.8, 3.9]
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Upgrade setuptools
+        run: |
+          pip3 install wheel --upgrade
+          pip3 install setuptools --upgrade
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install cryoDRGN with dev dependencies
+        run: |
+          python -m pip install .[dev]
+
+      - name: Pytest
+        run: |
+          pytest

README.md

@@ -1,3 +1,5 @@
+[![CI](https://github.com/zhonge/cryodrgn/actions/workflows/main.yml/badge.svg)](https://github.com/zhonge/cryodrgn/actions/workflows/main.yml)
+
 # :snowflake::dragon: cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction
 
 CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a *continuous* distribution over 3D structures by using a neural network based representation for the volume.
@@ -12,13 +14,14 @@ Reconstructing continuous distributions of 3D protein structure from cryo-EM ima
 Ellen D. Zhong, Tristan Bepler, Joseph H. Davis*, Bonnie Berger*.
 ICLR 2020, Spotlight presentation, https://arxiv.org/abs/1909.05215
 
-## Tutorial:
 
-An online overview and walkthrough of cryoDRGN installation, training, and analysis is available here:
-https://www.notion.so/cryoDRGN-tutorial-b932c021cb2c415282f182048bac16ff
+## Documentation:
+
+The latest documentation for cryoDRGN is available [here](https://zhonge.github.io/cryodrgn/). This includes an overview and walkthrough of cryoDRGN installation, training and analysis.
+
+A more in-depth manuscript version of the tutorial is available [here](https://www.biorxiv.org/content/10.1101/2022.08.09.503342v1).
 
-A more in-depth manuscript version of the tutorial is available here: 
-https://www.biorxiv.org/content/10.1101/2022.08.09.503342v1
+Old Documentation pages are available at [notion.so](https://www.notion.so/cryoDRGN-tutorial-b932c021cb2c415282f182048bac16ff).
 
 A quick start is provided below.
 
@@ -102,7 +105,7 @@ The official version 1.0 release. This version introduces several new tools for
 
 <details><summary>Version 0.2.0</summary>
 
-* New interface and proper python packaing with setup.py. This version has identical functionality and argument usage as previous versions, however tools are now available from a common entry point. See:
+* New interface and proper python packaging with `setup.py`. This version has identical functionality and argument usage as previous versions, however tools are now available from a common entry point. See:
 
     `$ cryodrgn <command> -h`
 
@@ -135,7 +138,7 @@ To install cryoDRGN, git clone the source code and install the following depende
     git clone https://github.com/zhonge/cryodrgn.git
     cd cryodrgn
     git checkout 1.1.0 # or latest version
-    python setup.py install
+    pip install .
 
 A detailed installation and testing guide is provided here: https://www.notion.so/cryoDRGN-installation-with-anaconda-4cff0367d9b241bb8d902efe339d01e6
 

cryodrgn/__init__.py

@@ -1,4 +1,11 @@
 import os
 
-__version__ = '1.1.0'
+# The _version.py file is managed by setuptools-scm
+#   and is not in version control.
+try:
+    from ._version import version as __version__
+except ModuleNotFoundError:
+    # We're likely running as a source package without installation
+    __version__ = 'src'
+
 _ROOT = os.path.abspath(os.path.dirname(__file__))

cryodrgn/commands_utils/write_star.py

@@ -120,7 +120,7 @@ def main(args):
         for i in range(2):
             data[POSE_HDRS[3+i]] = trans[:,i]
     df = pd.DataFrame(data=data) 
-    headers = HEADERS + POSE_HDRS if args.poses else HEADERS
+    headers = HEADERS + POSE_HDRS if args.poses else HEADERS.copy()
 
     if args.keep_micrograph:
         assert args.ref_star, "Must provide reference .star file with micrograph coordinates"

cryodrgn/utils.py

@@ -160,3 +160,11 @@ def zero_sphere(vol):
     vol[tmp] = 0
     return vol
 
+def assert_pkl_close(pkl_a, pkl_b, atol=1e-4):
+    a = pickle.load(open(pkl_a, 'rb'))
+    b = pickle.load(open(pkl_b, 'rb'))
+    if isinstance(a, tuple):
+        for _a, _b in zip(a, b):
+            assert np.linalg.norm(_a - _b) < atol
+    else:
+        assert np.linalg.norm(a - b) < atol

docs/Makefile

@@ -0,0 +1,24 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+HTMLCOPYDIR   = _build/html
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+ifneq ("$(HTMLCOPYDIR)", "$(BUILDDIR)/html")
+	cp -rT $(BUILDDIR)/html $(HTMLCOPYDIR)
+endif

docs/conf.py

@@ -0,0 +1,33 @@
+# 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 = 'CryoDRGN'
+copyright = '2022, Ellen Zhong'
+author = 'Ellen Zhong'
+release = '1.1.1'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ['myst_parser']
+
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown',
+}
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_book_theme'
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,26 @@
+.. CryoDRGN documentation master file, created by
+   sphinx-quickstart on Mon Sep 12 11:12:23 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to CryoDRGN's documentation!
+====================================
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Contents:
+
+   pages/intro
+   pages/installation
+   pages/empiar_tutorial
+   pages/landscape_analysis
+   pages/large_datasets
+   pages/faq
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+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