Merge branch 'develop' into cleanup

.github/workflows/config/make.inc.gfort

@@ -8,8 +8,8 @@ F90 = gfortran
 #MPIF90 = mpgfortran #mpif90
 
 # Options for debugging  When we move to 4.9 add -fsanitize=leak
-FCOPTS = -fprofile-arcs -ftest-coverage  -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace -std=f2008
-LDOPTS = -fprofile-arcs -ftest-coverage -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace -std=f2008
+FCOPTS = -fprofile-arcs -ftest-coverage  -fstrict-aliasing  -fno-omit-frame-pointer -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace -std=f2008 -DW90DEV
+LDOPTS = -fprofile-arcs -ftest-coverage -fstrict-aliasing  -fno-omit-frame-pointer -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace -std=f2008
 
 #=======================
 # System LAPACK and BLAS

.github/workflows/config/make.inc.gfort+openmpi

@@ -8,8 +8,8 @@ COMMS  = mpi
 MPIF90 = mpif90 
 
 # Options for debugging  When we move to 4.9 add -fsanitize=leak
-FCOPTS = -fprofile-arcs -ftest-coverage  -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace 
-LDOPTS = -fprofile-arcs -ftest-coverage -fstrict-aliasing  -fno-omit-frame-pointer -fno-realloc-lhs -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace 
+FCOPTS = -fprofile-arcs -ftest-coverage  -fstrict-aliasing  -fno-omit-frame-pointer -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace -DW90DEV
+LDOPTS = -fprofile-arcs -ftest-coverage -fstrict-aliasing  -fno-omit-frame-pointer -fcheck=bounds,do,recursion,pointer -ffree-form -Wall -Waliasing -Wsurprising -Wline-truncation -Wno-tabs -Wno-uninitialized -Wno-unused-dummy-argument -Wno-unused -Wno-character-truncation -O1 -g -fbacktrace 
 
 #=======================
 # System LAPACK and BLAS

.github/workflows/main.yml

@@ -4,8 +4,8 @@ on:
   pull_request:
   push:
     branches:
-    - develop
-    
+      - develop
+
 jobs:
   pre-commit:
     runs-on: ubuntu-20.04
@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        w90-binary-parallel: [ 'false', 'true' ]
+        w90-binary-parallel: ["false", "true"]
     name: Build and test `parallel=${{ matrix.w90-binary-parallel }}`
     steps:
       - name: checkout
@@ -30,7 +30,7 @@ jobs:
       - name: install dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install  \
+          sudo apt-get -y install  \
             gfortran            \
             libblas-dev         \
             liblapack-dev       \
@@ -66,3 +66,23 @@ jobs:
           path: |
             test-suite/tests/test*/test.err*
             test-suite/tests/test*/test.out*
+
+  docs:
+    name: Validate mkdocs links
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          # use the latest stable version
+          python-version: "3.x"
+          cache: "pip"
+      # `pybtex` uses `pkg_resources` which is deprecated. Use workaround until upstream `mkdocs_bibtext`decides on a solution
+      # https://github.com/shyamd/mkdocs-bibtex/issues/228
+      # https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
+      - run: pip install -r docs/requirements.txt setuptools
+      - run: mkdocs build --strict
+        working-directory: ./docs
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          ENABLE_MKDOCS_GIT_COMMITTERS: False

.github/workflows/run_tests.sh

@@ -6,22 +6,6 @@ TESTDIR=$(pwd)/test-suite/
 echo $TESTDIR
 cd "$TESTDIR"
 
-echo "****************************************"
-echo "* RUNNING SERIAL TEST FOR LIBRARY MODE *"
-echo "****************************************"
-cd library-mode-test
-# Create the binary for testing
-make
-# remove the output file from old runs, if there
-rm -f results.dat
-# Run it - if it crashes it should give a non-zero error
-./test_library_serial.x
-# Check the output values
-./compare_results.py
-
-## Going back to the test dir
-cd "$TESTDIR"
-
 # Default: serial, no mpirun. Run these in any case
 echo "************************"
 echo "* RUNNING SERIAL TESTS *"

.gitignore

@@ -11,3 +11,4 @@ libwannier.dylib
 *~
 *.x.dSYM
 .vscode
+*.mod

.markdownlint.yaml

@@ -0,0 +1,25 @@
+# config file markdownlint-cli2
+
+# MD007/ul-indent : Unordered list indentation : https://github.com/DavidAnson/markdownlint/blob/main/doc/md007.md
+# this is to make sure mkdocs can correctly render nested lists
+MD007:
+  # Spaces for indent
+  indent: 4
+
+# MD033/no-inline-html : Inline HTML : https://github.com/DavidAnson/markdownlint/blob/v0.33.0/doc/md033.md
+MD033:
+  allowed_elements:
+    - br
+    - figure
+    - table
+    - figcaption
+    - em
+    - sub
+    - a
+    - sup
+    - code
+
+# MD046/code-block-style : https://github.com/DavidAnson/markdownlint/blob/v0.33.0/doc/md046.md
+# for code blocks in list https://github.com/DavidAnson/markdownlint/issues/327
+MD046:
+  style: fenced

.pre-commit-config.yaml

@@ -3,18 +3,27 @@ repos:
   rev: v4.1.0
   hooks:
   - id: check-yaml
+    exclude: (?x)^(
+        docs/mkdocs.yml
+      )$
+  - id: check-yaml
+    name: check yaml unsafe
+    args: ['--unsafe']
+    files: (?x)^(
+        docs/mkdocs.yml
+      )$
   - id: trailing-whitespace
     files: (?x)^(
         Makefile|
         config/make[.]inc[.\w]*|
-        examples/example\d\d[-]?\w*/.+win|
+        tutorials/tutorial\d\d[-]?\w*/.+win|
         src/.+
       )$
   - id: end-of-file-fixer
     files: (?x)^(
         Makefile|
         config/make[.]inc[.\w]*|
-        examples/example\d\d[-]?\w*/.+win|
+        tutorials/tutorial\d\d[-]?\w*/.+win|
         src/.+
       )$
 - repo: https://github.com/pseewald/fprettify
@@ -26,3 +35,11 @@ repos:
         pwscf/.*
       )$
     verbose: true
+- repo: https://github.com/DavidAnson/markdownlint-cli2
+  rev: v0.12.1
+  hooks:
+  - id: markdownlint-cli2
+    args: ['--fix']
+    files: (?x)^(
+        docs/.*
+      )$

.readthedocs.yaml

@@ -0,0 +1,17 @@
+# Read the Docs configuration file for MkDocs projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    # latest 3.x version available on Read the Docs
+    python: "3"
+
+mkdocs:
+  configuration: docs/mkdocs.yml
+
+python:
+  install:
+  - requirements: docs/requirements.txt

Makefile

@@ -83,22 +83,19 @@ clean:
 		$(MAKE) -f $(REALMAKEFILE) clean && \
 		cd ../ && rm -rf obj ; \
 	fi )
-	$(MAKE) -C $(ROOTDIR)/doc/user_guide clean
-	$(MAKE) -C $(ROOTDIR)/doc/tutorial clean
+	cd $(ROOTDIR)/docs && rm -r site
 	$(MAKE) -C $(ROOTDIR)/utility/w90pov clean
 	$(MAKE) -C $(ROOTDIR)/utility/w90vdw clean
 	cd $(ROOTDIR)/test-suite && ./clean_tests
 
 veryclean: clean
 	cd $(ROOTDIR) && rm -f wannier90.x postw90.x libwannier.a libwan2.a w90chk2chk.x w90spn2spn.x
-	cd $(ROOTDIR)/doc && rm -f user_guide.pdf tutorial.pdf
-	cd $(ROOTDIR)/doc/user_guide && rm -f user_guide.ps
-	cd $(ROOTDIR)/doc/tutorial && rm -f tutorial.ps
+	cd $(ROOTDIR)/docs && rm -r site
 	cd $(ROOTDIR)/test-suite && ./clean_tests -i
 
 thedoc:
-	$(MAKE) -C $(ROOTDIR)/doc/user_guide
-	$(MAKE) -C $(ROOTDIR)/doc/tutorial
+	@(echo "The latex user_guide and tutorials have been migrated to markdown \
+	format, for more details see 'docs/README.md' file.")
 
 # For now hardcoded to 3.1.0, and using HEAD
 # Better to get the version from the io.F90 file and use

README.rst

@@ -5,13 +5,18 @@ Wannier90
 The Maximally-Localised Generalised Wannier Functions Code 
 ----------------------------------------------------------
 
-The homepage of the Wannier90 code is http://www.wannier.org
+The homepage of the Wannier90 code is https://www.wannier.org
 
 The code is hosted on 
 GitHub_.
 
+The documentation of the code can be found
+here_.
+
 .. _GitHub: https://github.com/wannier-developers/wannier90
 
+.. _here: https://wannier90.readthedocs.io/
+
 How to contribute
 +++++++++++++++++
 
@@ -87,14 +92,20 @@ Authors and contributors
 
 The Wannier90 Developer Group includes:
 
-* Giovanni Pizzi    (EPFL, CH)
-* Valerio Vitale    (Cambridge, GB)
+* Giovanni Pizzi    (Paul Scherrer Institute, CH)
+* Valerio Vitale    (University of Trieste, IT)
 * David Vanderbilt  (Rutgers University, US)
 * Nicola Marzari    (EPFL, CH)
 * Ivo Souza         (Universidad del Pais Vasco, ES)
 * Arash A. Mostofi  (Imperial College London, GB)
 * Jonathan R. Yates (University of Oxford, GB)
 
+In addition to the Wannier90 Developer Group, the other authors of Wannier90 v.4.x are:
+
+* Jerome Jackson    (STFC Daresbury Laboratory, UK): CCP9 code restructuring and parallel library design
+* Leon Petit        (STFC Daresbury Laboratory, UK): CCP9 code restructuring and parallel library design
+* Barry G. Searle   (STFC Daresbury Laboratory, UK): CCP9 code restructuring and parallel library design, python interface
+
 In addition to the Wannier90 Developer Group, the other authors of Wannier90 v.3.x are:
 
 * Ryotaro Arita (Riken and U. Tokyo, JP): Symmetry-adapted Wannier functions
@@ -117,6 +128,7 @@ In addition to the Wannier90 Developer Group, the other authors of Wannier90 v.3
 * Lorenzo Paulatto (Sorbonne Paris, FR): Improvements to the interpolation routines, non-collinear spin with ultrasoft in pw2wannier90
 * Samuel Poncé (Oxford University, GB): Test suite for Wannier90
 * Thomas Ponweiser (RISC Software GmbH, AT): performance optimizations for postw90
+* Junfeng Qiao (EPFL, CH): spin Hall conductivity
 * Florian Thöle (ETHZ, CH): non-collinear spin with ultrasoft in pw2wannier90
 * Stepan Tsirkin (Universidad del Pais Vasco, ES): GW bands interpolation, gyrotropic module, shift-current calculation, bug fixes in the berry module
 * Małgorzata Wierzbowska (Polish Academy of Science, PL): performance optimizations for postw90