Merge pull request #56 from Tieqiong/ipynb

Add ipynb outputs and data, pcmt, workflows

Author: sbillinge

.github/workflows/build-wheel-release-upload.yml

@@ -3,6 +3,8 @@ name: Release (GitHub/PyPI) and Deploy Docs
 on:
   workflow_dispatch:
   push:
+    branches:
+      - "**"
     tags:
       - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 

.github/workflows/tests-on-pr.yml

@@ -2,6 +2,8 @@ name: Tests on PR
 
 on:
   pull_request:
+    branches:
+      - "**"
   workflow_dispatch:
 
 jobs:

.pre-commit-config.yaml

@@ -33,10 +33,11 @@ repos:
     hooks:
       - id: isort
         args: ["--profile", "black"]
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
-    hooks:
-      - id: nbstripout
+  # disable nbstripout to preserve examples ipynb outputs
+  # - repo: https://github.com/kynan/nbstripout
+  #   rev: 0.7.1
+  #   hooks:
+  #     - id: nbstripout
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
@@ -48,8 +49,32 @@ repos:
     rev: v2.3.0
     hooks:
       - id: codespell
+        exclude: '.*\.ipynb$'
         additional_dependencies:
           - tomli
+  # nbQA for ipynb dedicated codespell
+  - repo: https://github.com/nbQA-dev/nbQA
+    rev: 1.9.1
+    hooks:
+      - id: nbqa
+        entry: nbqa codespell
+        name: nbqa-codespell-code
+        alias: nbqa-codespell-code
+        types: [jupyter]
+        additional_dependencies:
+          - codespell==2.3.0
+        args:
+          - "--nbqa-shell"
+      - id: nbqa
+        entry: nbqa codespell
+        name: nbqa-codespell-md
+        alias: nbqa-codespell-md
+        types: [jupyter]
+        additional_dependencies:
+          - codespell==2.3.0
+        args:
+          - "--nbqa-shell"
+          - "--nbqa-md"
   # prettier - multi formatter for .json, .yml, and .md files
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8

README.rst

@@ -153,4 +153,13 @@ For more information on pyobjcryst please visit the project `web-page <https://d
 Acknowledgements
 ----------------
 
+This package bundles the following IUCr data files for bona fide research use:
+
+- **cpd-1a.prn:** Powder diffraction dataset from the `IUCr CPD Round Robin on Quantitative Phase Analysis <https://www.iucr.org/__data/iucr/powder/QARR/index.html>`_.
+
+  Source: https://www.iucr.org/__data/iucr/powder/QARR/col/cpd-1a.prn
+
+  Round Robin on Quantitative Phase Analysis: Madsen, I. (1997) ‘Round Robin on Quantitative Phase Analysis’, Powder Diffraction, 12(1), pp. 1–2. Available at: https://doi.org/10.1017/S0885715600020212.
+
+
 ``pyobjcryst`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.

examples/QPA-Quantitative phase analysis.ipynb

@@ -0,0 +1,19 @@
+KEYWORDS GO HERE
+17
+C  1
+N   1 1.465
+C   2 1.366  1 119.987
+N   3 1.321  2 120.030  1   6.0
+C   4 1.355  3 119.982  2   6.8
+N   5 1.136  4 180.000  3  46.3
+N   3 1.366  2 120.022  1 186.0
+C   7 1.466  3 119.988  2 354.9
+C   8 1.529  7 109.482  3 185.0
+S   9 1.814  8 109.456  7 180.0
+C  10 1.815  9  99.984  8 180.0
+C  11 1.507 10 109.466  9 180.0
+N  12 1.341 11 126.014 10  90.0
+C  13 1.305 12 109.239 11 180.0
+N  14 1.349 13 108.723 12 360.0
+C  15 1.344 14 107.593 13 359.1
+C  16 1.515 15 127.952 14 179.1