Add demo (#15)

* adding demo; update readme with typical installation time * update demo briefly on how to run on own data; update readme for system requrements and system versions * fix links * Fine-tune notebook and add to docs * Embed images * Tweak styling * Fix formatting and typos Co-authored-by: BinWang <[email protected]>
instamatic-dev · May 9, 2022 · a2c5344 · a2c5344
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diff --git a/.gitignore b/.gitignore
@@ -2,14 +2,37 @@
 *.bpc
 *.c
 *.dacs
-*.egg-info
 *.log
 *.pptx
 *.prefs
-*.pyc
-*.pyd
 *.txt
 *.zip
-.coverage
 .db
 
+*.py[cod]
+*.egg-info
+*.eggs
+.ipynb_checkpoints
+*.vtk
+
+build
+dist
+.cache
+__pycache__
+
+htmlcov
+.coverage
+coverage.xml
+.pytest_cache
+
+docs/_build
+docs/apidocs
+playground/
+
+# ide
+.idea
+.eclipse
+.vscode
+
+# Mac
+.DS_Store
diff --git a/README.md b/README.md
@@ -8,7 +8,9 @@
 
 Collection of tools for automated processing and clustering of single-crystal electron diffraction data.
 
-Install using `pip install edtools`.
+Install using `pip install edtools`. Installation should take less than 20 seconds on a normal desktop.
+
+Find the latest [releases](https://github.com/instamatic-dev/edtools/releases) for the versions that have been tested on.
 
 [The source for this project is available here][src].
 
@@ -32,7 +34,7 @@ Looks files matching `CORRECT.LP` in all subdirectories and extracts unit cell/i
 
 ### find_cell.py
 
-This program a cells.yaml file and shows histogram plots with the unit cell parameters. This program mimicks `CELLPARM` (http://xds.mpimf-heidelberg.mpg.de/html_doc/cellparm_program.html) and calculates the weighted mean lattice parameters, where the weight is typically the number of observed reflections (defaults to 1.0). For each lattice parameter, the mean is calculated in a given range (default range = median+-2). The range can be changed by dragging the cursor on the histogram plots.
+This program a cells.yaml file and shows histogram plots with the unit cell parameters. This program mimicks [`CELLPARM`](http://xds.mpimf-heidelberg.mpg.de/html_doc/cellparm_program.html) and calculates the weighted mean lattice parameters, where the weight is typically the number of observed reflections (defaults to 1.0). For each lattice parameter, the mean is calculated in a given range (default range = median+-2). The range can be changed by dragging the cursor on the histogram plots.
 
 Alternatively, the unit cells can be clustered by giving the `--cluster` command, in which a dendrogram is shown. The cluster cutoff can be selected by clicking in the dendrogram. The clusters will be written to `cells_cluster_#.yaml`.
 
@@ -109,13 +111,19 @@ Usage:
 edtools.find_rotation_axis [XDS.INP]
 ```
 
+## OS Requirement
+
+The package has been mainly developed and tested under windows 10.
 
-## Requirements
+## Software Requirements
 
-- Python3.6 including `numpy`, `scipy`, `matplotlib`, and `pandas` libraries
+- Python 3.6+ including `numpy`, `scipy`, `matplotlib`, and `pandas` libraries
 - `sginfo` or `cctbx.python` must be available on the system path for `edtools.make_shelx`
-- (Windows 10) Access to [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux)
-- (Windows 10) XDS and related tools must be available under WSL
+- (Windows 10 or newer) Access to [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux)
+- (Windows 10 or newer) XDS and related tools must be available under WSL
+
+## Package dependencies
 
+Check [pyproject.toml](pyproject.toml) for the full dependency list and versions.
 
 [src]: https://github.com/instamatic-dev/edtools
diff --git a/docs/conf.py b/docs/conf.py
@@ -54,6 +54,7 @@ def setup(app):
     # 'nbsphinx_link',
     # 'sphinx.ext.todo',
     # 'sphinx.ext.viewcode',
+    'nbsphinx',
     'autodocsumm',
 ]
 

diff --git a/docs/examples/edtools_demo.ipynb b/docs/examples/edtools_demo.ipynb
diff --git a/docs/examples/find_cell_step3.png b/docs/examples/find_cell_step3.png
diff --git a/docs/examples/find_cell_step5.png b/docs/examples/find_cell_step5.png
diff --git a/docs/examples/intensity_cluster.png b/docs/examples/intensity_cluster.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -12,6 +12,16 @@ API Reference
    edtools
 
 
+Examples
+========
+.. toctree::
+   :maxdepth: 1
+   :caption: Examples
+   :glob:
+
+   examples/*
+
+
 Links
 =====
 .. toctree::

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,5 +1,6 @@
 sphinx
 sphinx_rtd_theme
+nbsphinx
 readthedocs-sphinx-search
 autodocsumm
 lmfit