Add gh action

.github/workflows/tests.yml

@@ -0,0 +1,73 @@
+# Based on https://github.com/executablebooks/cookiecutter-jupyter-book/blob/main/.github/workflows/tests.yml
+name: tests
+
+on:
+  # Trigger the workflow on push or pull request on main branch
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  schedule:
+    # Run cron job every month, https://crontab.guru/every-month
+    - cron: '0 0 1 * *'
+  workflow_dispatch:
+
+jobs:
+  # This job tests that the CC works
+  test-cc-and-jb-build:
+    # prevent this action from running on forks
+    #if: github.repository == 'abinit/abipy'
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
+
+    runs-on: ubuntu-latest
+    #env:
+    #  PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
+
+    # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+    permissions:
+      pages: write
+      id-token: write
+
+    steps:
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+          auto-update-conda: true
+
+    # Install dependencies
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.11
+    - name: Install Abinit, AbiPy and dependencies
+      run: |
+        conda create -n abipy python=${{ matrix.config.python }} --yes
+        conda activate abipy
+        conda install abinit -c conda-forge --yes
+        mpirun -n 1 abinit --version
+        mpirun -n 1 abinit --build
+        pip install --editable .
+        mkdir -p $HOME/.abinit/abipy/
+        #cp abipy/data/managers/travis_manager.yml $HOME/.abinit/abipy/manager.yml
+        #cp abipy/data/managers/simple_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
+        jupyter-book build abipy_book --builder linkcheck
+
+    # Build the example book
+    #- name: Build book
+    #  run: |
+    #    jupyter-book build my_book/my_book/
+
+    ## Upload the book's HTML as an artifact
+    #- name: Upload artifact
+    #  uses: actions/upload-pages-artifact@v2
+    #  with:
+    #    path: "my_book/my_book/_build/html"
+
+    # Deploy the book's HTML to GitHub Pages
+    #- name: Deploy to GitHub Pages
+    #  id: deployment
+    #  uses: actions/deploy-pages@v2

.gitignore

@@ -4,6 +4,7 @@ Profile.prof
 abipy/examples/flows/flow_*
 abipy/examples/flows/develop/flow_*
 _debug
+_build
 #__abinb_workdir__
 #abinb_*.ipynb
 $*.pickle

abipy_book/README.md

@@ -1,5 +1,5 @@
 
-# Documentation Howto 
+# Documentation Howto
 
 To insert a link to an Abinit variable, use:
 
@@ -9,10 +9,10 @@ or:
 
     {{asr_anaddb}}
 
-if you want to refer to the asr variable of the anaddb code 
+if you want to refer to the asr variable of the anaddb code
 (note that in abimkdocs one uses asr@anaddb but, unfortunately this syntax is not supported my MyST).
 
-There are several other replacements defined in _config.yml, mainly for links 
+There are several other replacements defined in _config.yml, mainly for links
 to the abipy documentation, python libraries and other useful websites.
 Also in this case, the syntax is:
 

abipy_book/abinit_input.md

@@ -172,7 +172,7 @@ The `set_structure` method sets the value of the ABINIT variables:
 
 It is always a good idea to set the structure immediately after the creation of an `AbinitInput`
 because several methods use this information to facilitate the specification of other variables.
-For instance, the `set_kpath` method uses the structure to generate the high-symmetry $k$-path 
+For instance, the `set_kpath` method uses the structure to generate the high-symmetry $k$-path
 for band structure calculations.
 
 ```{warning}
@@ -186,7 +186,7 @@ for band structure calculations.
 It is possible to create a structure in different ways.
 
 The most explicit (and verbose) consists in passing a dictionary with ABINIT variables
-provided one uses python lists (or lists or lists) when ABINIT expects a 1D 
+provided one uses python lists (or lists or lists) when ABINIT expects a 1D
 (or a multidimensional array):
 
 
@@ -208,7 +208,7 @@ print(si_struct)
 
 +++
 
-If you already have a string with the Abinit variable, you can use the `from_abistring` class method: 
+If you already have a string with the Abinit variable, you can use the `from_abistring` class method:
 
 ```{code-cell}
 lif_struct = abilab.Structure.from_abistring("""
@@ -228,9 +228,9 @@ print(lif_struct)
 ```
 
 This approach requires less input yet we still need to specify {{ntypat}}, {{znucl}}and {[typat}}.
-Fortunately, *from_abistring* supports another Abinit-specific format in which the 
+Fortunately, *from_abistring* supports another Abinit-specific format in which the
 fractional coordinates and the element symbol are specified via the *xred_symbols* variable.
-In this case {{ntypat}}, {{znucl}} and {{typat}} do not need to be specified as they are automatically 
+In this case {{ntypat}}, {{znucl}} and {{typat}} do not need to be specified as they are automatically
 computed from *xred_symbols*:
 
 

abipy_book/abiwan.md

@@ -20,7 +20,7 @@ produced by Abinit to interpolate band energies.
 As usual, one can use:
 
     abiopen.py FILE_ABIWAN.nc
-    
+
 with the `--expose` or the `--print` option for a command line interface
 and `--notebook` to generate a jupyter notebook.
 
@@ -37,7 +37,7 @@ Let's start by importing the basic modules needed for this tutorial.
 ```{code-cell} ipython3
 import os
 
-import warnings 
+import warnings
 warnings.filterwarnings("ignore")  # Ignore warnings
 
 from abipy import abilab
@@ -46,13 +46,13 @@ import abipy.data as abidata
 
 # This line configures matplotlib to show figures embedded in the notebook.
 # Replace `inline` with `notebook` in classic notebook
-%matplotlib inline   
+%matplotlib inline
 
 # Option available in jupyterlab. See https://github.com/matplotlib/jupyter-matplotlib
-#%matplotlib widget  
+#%matplotlib widget
 ```
 
-## How to analyze the WOUT file  
+## How to analyze the WOUT file
 
 +++
 
@@ -105,7 +105,7 @@ To plot the matrix elements of the KS Hamiltonian in real space in the Wannier G
 abiwan.hwan.plot(title="Matrix elements in real space");
 ```
 
-To interpolate the KS energies along a high-symmetry k-path and construct 
+To interpolate the KS energies along a high-symmetry k-path and construct
 a new `ElectronBands` object, use:
 
 ```{code-cell} ipython3
@@ -129,12 +129,12 @@ ebands_kpath.plot_with_edos(ebands_kmesh.get_edos(), title="Wannier-interpolated
 ```
 
 We can also compare an ab-initio band structure with the Wannier-interpolated results.
-This is useful to understand if our wannier functions are well localized and if the 
+This is useful to understand if our wannier functions are well localized and if the
 k-mesh used with wannier90 is dense enough.
 
-In this case, it is just a matter of passing the path to the netcdf file 
+In this case, it is just a matter of passing the path to the netcdf file
 containing the ab-initio band structure to the `get_plotter_from_ebands` method of `abiwan`.
-The function interpolates the band energies using the k-path found in the netcdf file 
+The function interpolates the band energies using the k-path found in the netcdf file
 and returns a plotter object:
 
 ```{code-cell} ipython3
@@ -151,7 +151,7 @@ plotter.combiplot();
 ```
 
 As we can see, the interpolated band structures is not completely on top of the ab-initio
-results. To improve the agreement we should try to reduced the spread and/or increase 
+results. To improve the agreement we should try to reduced the spread and/or increase
 the density of the k-mesh used in the wannierization procedure.
 
 +++