Merge branch 'develop' of github.com:abinit/abipy into develop

pull trunk develop

Author: VicTrqt

.github/workflows/gh-pages.yml

@@ -2,7 +2,7 @@ name: Deploy documentation with GitHub Pages dependencies preinstalled
 
 on:
   push:
-    branches: ["develop"]
+    branches: ["develop", "master"]
   workflow_dispatch: # enable manual workflow execution
 
 # Set permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
@@ -57,24 +57,30 @@ jobs:
             conda install abinit -c conda-forge --yes
             mpirun -n 1 abinit --version
             mpirun -n 1 abinit --build
+
+            # Update submodules with data.
+            git submodule update --remote --init
+            git submodule update --recursive --remote
+
             pip install --editable .
             mkdir -p $HOME/.abinit/abipy/
             cp abipy/data/managers/gh_manager.yml $HOME/.abinit/abipy/manager.yml
             cp abipy/data/managers/gh_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
-            # FIXME TEMPORARY HACK
-            pip install git+https://github.com/gmatteo/pymatgen.git@master -U
+
+            # TEMPORARY HACK THAT MIGHT BE NEEDED IF THE PYMATGEN GUYS BREAK STUFF
+            #pip install git+https://github.com/gmatteo/pymatgen.git@master -U
 
       - name: Build docs with Sphinx
         run: |
             conda activate abipy
             cd docs
             source install.sh
-            make
+            make -j
 
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v2
         with:
-          path: site/ # Important. Set to your output dir in MkDocs
+          path: docs/_build/html/ # Important. Set to the website output dir
 
   deploy:
     environment:

.github/workflows/test.yml

@@ -3,8 +3,10 @@ name: Run the Abipy test suite.
 on:
   push:
     branches: [develop, master]
+    paths-ignore: ["**/*.md", docs/**]
   pull_request:
     branches: [develop]
+    paths-ignore: ["**/*.md", docs/**]
   workflow_dispatch:
   workflow_call: # make this workflow reusable by release.yml
 
@@ -14,7 +16,7 @@ permissions:
 jobs:
   test:
     # prevent this action from running on forks
-    #if: github.repository == 'abinit/abipy'
+    if: github.repository == 'abinit/abipy'
     defaults:
       run:
         shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
@@ -24,17 +26,17 @@ jobs:
       matrix:
         config:
           - os: ubuntu-latest
-            python: '3.11'
-        config:
+            python: "3.11"
           - os: ubuntu-latest
-            python: '3.12'
+            python: "3.12"
 
     runs-on: ${{ matrix.config.os }}
+
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
 
     steps:
-      - name: Check out Abipy repo
+      - name: Checkout Abipy repo
         uses: actions/checkout@v4
 
       - name: Set up Miniconda
@@ -49,11 +51,20 @@ jobs:
             conda install abinit -c conda-forge --yes
             mpirun -n 1 abinit --version
             mpirun -n 1 abinit --build
+
+            # Update submodules with data.
+            git submodule update --remote --init
+            git submodule update --recursive --remote
+
+            pip install -r requirements.txt
+            pip install -r requirements-optional.txt
+            pip install -r requirements-panel.txt
             pip install --editable .
             mkdir -p $HOME/.abinit/abipy/
             cp abipy/data/managers/gh_manager.yml $HOME/.abinit/abipy/manager.yml
             cp abipy/data/managers/gh_scheduler.yml $HOME/.abinit/abipy/scheduler.yml
-            # FIXME TEMPORARY HACK
+
+            # TEMPORARY HACK THAT MIGHT BE NEEDED IF THE PYMATGEN GUYS BREAK STUFF
             #pip install git+https://github.com/gmatteo/pymatgen.git@master -U
 
       - name: pytest

.gitignore

@@ -3,7 +3,9 @@ abinit_vars.pickle
 Profile.prof
 abipy/examples/flows/flow_*
 abipy/examples/flows/develop/flow_*
+__abipy_import.log
 _debug
+abipy/scripts/tests/test-output/
 #__abinb_workdir__
 #abinb_*.ipynb
 $*.pickle

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "abipy/data/data_v-ZSISA-QHA.git"]
+	path = abipy/data/data_v-ZSISA-QHA.git
+	url = https://github.com/abinit/data_v-ZSISA-QHA.git

README.rst

@@ -31,10 +31,7 @@ AbiPy can be used in conjunction with matplotlib_, pandas_, scipy_, seaborn_, ip
 thus providing a powerful and user-friendly environment for data analysis and visualization.
 
 To learn more about the integration between jupyter_ and AbiPy, visit `our collection of notebooks
-<https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/index.ipynb>`_
-or click the **Launch Binder** badge to start a Docker image with Abinit, AbiPy and all the other python dependencies
-required to run the code inside the jupyter notebooks.
-The notebook will be opened in your browser after building.
+<https://abinit.github.io/abipy_book/intro.html>`_
 
 AbiPy is free to use. However, we also welcome your help to improve this library by making your own contributions.
 Please report any bugs and issues at AbiPy's `Github page <https://github.com/abinit/abipy>`_.
@@ -75,9 +72,9 @@ python packages through `Anaconda <https://continuum.io/downloads>`_ (or conda).
 See `Installing conda`_ to install conda itself.
 We routinely use conda_ to test new developments with multiple Python versions and multiple virtual environments.
 
-Create a new conda_ environment based on python 3.11 (let's call it ``abienv``) with::
+Create a new conda_ environment based on python 3.12 (let's call it ``abienv``) with::
 
-    conda create --name abienv python=3.11
+    conda create --name abienv python=3.12
 
 and activate it with::
 
@@ -87,9 +84,11 @@ You should see the name of the conda environment in the shell prompt.
 
 Finally, install AbiPy with::
 
-    conda install abipy -c conda-forge
+    conda install abipy -c conda-forge --yes
 
-Please note that, at present, conda-forge does not provide executables 
+Please note that, it is also possible to install the abinit executables in the same enviroment using
+
+    conda install abinit -c conda-forge --yes
 
 Additional information on the steps required to install AbiPy with anaconda are available
 in the `anaconda howto <http://abinit.github.io/abipy/installation#anaconda-howto>`_.
@@ -113,7 +112,7 @@ For pip, use::
 
 If you are using conda_ (see `Installing conda`_ to install conda itself), create a new environment (``abienv``) with::
 
-    conda create -n abienv python=3.11
+    conda create -n abienv python=3.12
     source activate abienv
 
 Add ``conda-forge``, and ``abinit`` to your channels with::