Fix links

.github/workflows/tests.yml

@@ -16,7 +16,7 @@ on:
 
 jobs:
   # This job tests that the CC works
-  test-cc-and-jb-build:
+  test-and-jb-build:
     # prevent this action from running on forks
     #if: github.repository == 'abinit/abipy'
     defaults:
@@ -68,7 +68,7 @@ jobs:
       - name: Upload the book's HTML as an artifact
         uses: actions/upload-pages-artifact@v2
         with:
-          path: "abipy_book/abipy_book/_build/html"
+          path: abipy_book/abipy_book/_build/html
 
       # Deploy the book's HTML to GitHub Pages
       #- name: Deploy to GitHub Pages

abipy_book/_config.yml

@@ -101,7 +101,7 @@ sphinx:
           - "https://docs.scipy.org/doc/scipy/reference/"
           - null
         pandas:
-          - "http://pandas-docs.github.io/pandas-docs-travis/"
+          - "https://pandas.pydata.org/pandas-docs/stable/"
           - null
         matplotlib:
           - "https://matplotlib.org/"

abipy_book/elastic/lesson_elastic.md

@@ -252,8 +252,8 @@ The tensors are available as attributes of the `edata` object:
 edata.elastic_relaxed
 ```
 
-These are pymatgen [tensors](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/elasticity/tensors.py),
-more specifically [ElasticTensor objects](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/elasticity/elastic.py)
+These are pymatgen [tensors](https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/analysis/elasticity/tensors.py),
+more specifically [ElasticTensor objects](https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/analysis/elasticity/elastic.py)
 so we have access to several useful methods.
 To get the Voigt bulk modulus, use:
 
@@ -279,7 +279,7 @@ edata.get_elastic_properties_dataframe(properties_as_index=True)
 ```
 
 For the meaning of the different quantities please consult the
-[pymatgen module](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/analysis/elasticity/elastic.py).
+[pymatgen module](https://github.com/materialsproject/pymatgen/blob/master/src/pymatgen/analysis/elasticity/elastic.py).
 
 +++
 

abipy_book/eph_isotc/lesson_eph_isotc.md

@@ -173,10 +173,9 @@ The resolution in q-space can be improved by interpolating the DFPT potentials v
 
 The general theory of electron-phonon coupling and Eliashberg superconductivity is reviewed
 by P.B. Allen and B. Mitrovic
-in [Theory of Superconducting Tc](https://www.sciencedirect.com/science/article/pii/S0081194708606657).
+in [Theory of Superconducting Tc](https://doi.org/10.1016/S0081-1947(08)60665-7).
 The first implementations similar to that in Abinit are those in
-[Savrasov](https://doi.org/10.1103/PhysRevB.54.16487) and
-[Liu](https://doi.org/10.1103/PhysRevB.53.R7575).
+[Savrasov](https://doi.org/10.1103/PhysRevB.54.16487) and [Liu](https://doi.org/10.1103/PhysRevB.53.R7575).
 
 +++
 
@@ -257,8 +256,7 @@ in a single workflow the *electronic* properties, the *vibrational* spectrum
 and the *phonon linewidths* with different k-point samplings.
 
 Note that we have already encountered similar flows in the previous AbiPy lessons.
-The calculation of electronic band structures is
-discussed in
+The calculation of electronic band structures is discussed in
 [lesson_base3](https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/base3/lesson_base3.ipynb)
 while an example of `Flow` for phonon calculations is given in
 [lesson_dfpt](https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/dfpt/lesson_dfpt.ipynb).

abipy_book/intro.md

@@ -2,13 +2,13 @@
 
 Welcome to the AbiPy Jupyter Book!
 This book contains notebook-based documentation for [AbiPy](https://github.com/abinit/abipy).
-This augments our Sphinx-based [documentation](http://abinit.github.io/abipy>) with jupyter notebooks
+This augments our Sphinx-based [documentation](https://abinit.github.io/abipy>) with jupyter notebooks
 containing interactive tutorials and examples.
 
 Additional examples are available on the:
 
-* [AbiPy plot gallery](http://abinit.github.io/abipy/gallery/index.html)
-* [AbiPy flow gallery](http://abinit.github.io/abipy/flow_gallery/index.html)
+* [AbiPy plot gallery](https://abinit.github.io/abipy/gallery/index.html)
+* [AbiPy flow gallery](https://abinit.github.io/abipy/flow_gallery/index.html)
 * [Matgenb website](https://matgenb.materialsvirtuallab.org)
 
 Beginners should typically start with the three notebooks on Abipy objects,
@@ -19,31 +19,31 @@ and then examine the flows notebook.
 
 ## AbiPy Objects
 
-* [Structure](structure.html): The crystalline structure
-* [Abinit Input](abinit_input.html): How to create an `AbinitInput`
-* [Input Factories](input_factories.html): Generating input files for high-throughput calculations
+* [Structure](structure): The crystalline structure
+* [Abinit Input](abinit_input): How to create an `AbinitInput`
+* [Input Factories](input_factories): Generating input files for high-throughput calculations
 
 +++
 
 ## Output files supported by AbiPy
 
-* [GSR.nc](gsr.html): File with ground-state results produced by SCF/NSCF runs.
-* [HIST.nc](hist.html): File produced by structural relaxations and MD runs
-* [FATBANDS.nc](efatbands.html): Plot electronic fatbands and L-projected DOS
-* [DDB](ddb.html): Tools to analyze phonons
-* [SIGRES.nc](sigres.html): How to analyze the results of $GW$ calculations
-* [MDF.nc](mdf.html): How to analyze the results of Bethe-Salpeter calculations
-* [Lobster](lobster.html): How to analyze the output files produced by Lobster
-* [ABIWAN.nc](abiwan.html): How to analyze the Wannier90 wout file and the netcdf file produced by Abinit
+* [GSR.nc](gsr): File with ground-state results produced by SCF/NSCF runs.
+* [HIST.nc](hist): File produced by structural relaxations and MD runs
+* [FATBANDS.nc](efatbands): Plot electronic fatbands and L-projected DOS
+* [DDB](ddb): Tools to analyze phonons
+* [SIGRES.nc](sigres): How to analyze the results of $GW$ calculations
+* [MDF.nc](mdf): How to analyze the results of Bethe-Salpeter calculations
+* [Lobster](lobster): How to analyze the output files produced by Lobster
+* [ABIWAN.nc](abiwan): How to analyze the Wannier90 wout file and the netcdf file produced by Abinit
 
 +++
 
 ## AbiPy Workflows
 
-* [Flows](flows.html): How to automate calculations with `Flows`, `Works` and `Tasks`
+* [Flows](/flows.html): How to automate calculations with `Flows`, `Works` and `Tasks`
 
 This notebook is complemented with the documentation on the
-[TaskManager Configuration](http://abinit.github.io/abipy/workflows/taskmanager.html):
+[TaskManager Configuration](https://abinit.github.io/abipy/workflows/taskmanager.html):
 How to specify options in `manager.yml` and `scheduler.yml`
 
 +++