Decentralizing QE

codecov.yml → .github/codecov.yml

@@ -11,6 +11,3 @@ coverage:
     project: off
     patch: off
     changes: off
-
-ignore:
-  - "koopmans/testing"

.github/workflows/release.yml

@@ -0,0 +1,41 @@
+name: Publish
+
+on:
+  release:
+    types:
+    - published
+
+env:
+  GIT_USER_NAME: 'koopmans developers'
+  GIT_USER_EMAIL: ${{ secrets.PUBLISH_EMAIL }}
+
+jobs:
+
+  publish:
+    name: Publish koopmans
+    runs-on: ubuntu-latest
+    if: github.repository == 'epfl-theos/koopmans' && startsWith(github.ref, 'refs/tags/v')
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install Python dependencies
+      run: |
+        python -m pip install -U pip
+        pip install -U setuptools wheel build
+        pip install -e .
+
+    - name: Build source distribution
+      run: python -m build
+
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/typechecking.yml

@@ -33,4 +33,4 @@ jobs:
               pip install mypy
          - name: Run mypy
            run: |
-              mypy koopmans/ --ignore-missing-imports
+              mypy src/koopmans/ --ignore-missing-imports

.gitignore

@@ -27,3 +27,5 @@ postproc/
 wannier/
 screening/
 hamiltonian/
+build/
+dist/

.gitmodules

@@ -1,3 +1,9 @@
 [submodule "quantum_espresso/q-e"]
 	path = quantum_espresso/q-e
 	url = https://gitlab.com/QEF/q-e.git
+[submodule "quantum_espresso/kcp"]
+	path = quantum_espresso/kcp
+	url = ../koopmans-kcp.git
+[submodule "quantum_espresso/utils"]
+	path = quantum_espresso/utils
+	url = ../koopmans-qe-utils.git

.readthedocs.yml

@@ -19,7 +19,8 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
-    - requirements: docs/requirements.txt
-    - requirements: requirements/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

MANIFEST.in

@@ -0,0 +1,2 @@
+graft src/koopmans/pseudopotentials
+include src/koopmans/references.bib

Makefile

@@ -1,7 +1,10 @@
 # List of available tasks
-.PHONY: help install submodules configure_4 configure_7 configure espresso_4 espresso_7 espresso_utils espresso workflow tests clean clean_espresso clean_tests benchmarks
+.PHONY: help install submodules configure_4 configure_7 configure espresso_4 espresso_7 espresso_utils espresso espresso_4_install espresso_7_install espresso_utils_install espresso_install workflow tests clean clean_espresso clean_tests benchmarks
 
 MPIF90 = "mpif90"
+PREFIX ?= /usr/local
+
+default: submodules espresso workflow
 
 help:
 	@echo '  _                                                '
@@ -14,8 +17,9 @@ help:
 	@echo ' For performing Koopmans spectral functional calculations with Quantum ESPRESSO'
 	@echo ' See README.rst for more information'
 	@echo ''
-	@echo ' To install'
-	@echo ' > make install'
+	@echo ' To install everything'
+	@echo ' > make'
+	@echo ' > sudo make install'
 	@echo ' (For more details, see README.rst)'
 	@echo ''
 	@echo ' To run the test suite'
@@ -25,8 +29,6 @@ help:
 	@echo ' > make clean'
 	@echo ''
 
-install: submodules espresso workflow
-
 submodules:
 	git submodule init
 	git submodule update
@@ -40,16 +42,27 @@ configure_7:
 configure: configure_4 configure_7
 
 espresso_4:
-	@(cd quantum_espresso/kcp; $(MAKE) kcp)
+	@(cd quantum_espresso/kcp && $(MAKE) kcp)
+
+espresso_4_install:
+	@(cd quantum_espresso/kcp && $(MAKE) install PREFIX=$(PREFIX))
 
 espresso_7:
-	@(cd quantum_espresso/q-e; $(MAKE) pw kcw ph)
+	@(cd quantum_espresso/q-e && $(MAKE) pw kcw ph)
+
+espresso_7_install:
+	@(cd quantum_espresso/q-e && $(MAKE) install PREFIX=$(PREFIX))
 
 espresso_utils:
-	@(cd quantum_espresso/utils; $(MAKE) all)
+	@(cd quantum_espresso/utils && $(MAKE) all)
+
+espresso_utils_install:
+	@(cd quantum_espresso/utils && $(MAKE) install PREFIX=$(PREFIX))
 
 espresso: configure_4 espresso_4 configure_7 espresso_7 espresso_utils
 
+install: espresso_4_install espresso_7_install espresso_utils_install
+
 workflow:
 	python3 -m pip install --upgrade pip
 	python3 -m pip install -e .
@@ -67,5 +80,5 @@ tests:
 clean_tests:
 	rm -rf tests/tmp
 
-benchmark:
-	python3 -m pytest --generate_benchmark
+benchmarks:
+	python3 -m pytest tests/ --generate_benchmark

README.rst

@@ -12,7 +12,7 @@ This repository contains...
 
 | ``bin/`` executables (N.B. this directory does not need to be added to ``$PATH``)  
 | ``docs/`` documentation (see https://koopmans-functionals.org/)  
-| ``koopmans/`` source code of the workflow manager
+| ``src/`` source code
 | ``quantum_espresso/`` modified versions of ``Quantum ESPRESSO`` that contain implementations of the Koopmans functionals 
 | ``pseudos/`` pseudopotentials
 | ``requirements/`` python dependencies
@@ -24,7 +24,7 @@ Installation
 
 Quick installation
 ^^^^^^^^^^^^^^^^^^
-For a quick installation one can simply run ``make install``
+For a quick installation one can simply run ``make; sudo make install``
 
 Detailed installation
 ^^^^^^^^^^^^^^^^^^^^^
@@ -68,6 +68,17 @@ Then you need to compile the copies of ``Quantum ESPRESSO``. To do this, run
 
 where ``<mpif90>`` should be replaced by the name of your chosen MPI Fortran90 compiler e.g. ``MPIF90=mpiifort``. The code should automatically detect and link the requisite libraries. (If this fails you may need to manually compile the two versions of ``Quantum ESPRESSO`` contained in the ``quantum_espresso/`` directory.)
 
+Adding Quantum ESPRESSO to your path
+""""""""""""""""""""""""""""""""""""
+
+To add all of the Quantum ESPRESSO binaries to your path, run
+
+.. code-block:: bash
+
+   sudo make install
+
+By default this will copy the Quantum ESPRESSO binaries to ``/usr/local/bin``. This requires sudo privileges. If you do not have sudo privileges, you can either (a) install the codes in a different location by running ``make install PREFIX=/path/to/bin/`` (substitute ``/path/to/bin/`` with any directory of your choosing that is on your path) or (b) append ``bin/`` from the current directory to your path.
+
 Installing the workflow manager
 """""""""""""""""""""""""""""""
 
@@ -112,7 +123,7 @@ Currently, Koopmans functionals only works with norm-conserving pseudopotentials
 
 For convenience, ``koopmans`` already ships with both of these pseudopotential libraries and you can simply select the one you want to use using the ``pseudo_library`` keyword.
 
-If you prefer to use your own pseudopotentials, add them to ``koopmans/pseudopotentials`` in the subdirectory ``<my_pseudos>/<functional>``, where ``<my_pseudos>`` is a name of your choosing and ``<functional>`` is the functional used to generate your pseudopotentials. You can then direct ``koopmans`` to use these pseudopotentials by setting the keywords ``pseudo_library`` and ``base_functional`` to ``<my_pseudos>`` and ``<functional>`` respectively.
+If you prefer to use your own pseudopotentials, add them to ``src/koopmans/pseudopotentials/<my_pseudos>/<functional>``, where ``<my_pseudos>`` is a name of your choosing and ``<functional>`` is the functional used to generate your pseudopotentials. You can then direct ``koopmans`` to use these pseudopotentials by setting the keywords ``pseudo_library`` and ``base_functional`` to ``<my_pseudos>`` and ``<functional>`` respectively.
 
 Alternatively, you can direct the code to always use your personal pseudopotentials directory by defining the variable