Merge pull request #212 from timcallow/libxc_reqs_update

Simplify libxc installation

.github/workflows/gh-pages.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.12'
 
       - name: Upgrade pip
         run: python3 -m pip install --upgrade pip
@@ -44,7 +44,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.12'
 
       - name: Upgrade pip
         run: python3 -m pip install --upgrade pip

.github/workflows/tests.yml

@@ -21,7 +21,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.12'
 
       - name: Upgrade pip
         run: python -m pip install --upgrade pip
@@ -35,54 +35,12 @@ jobs:
           path: ~/.local/share/virtualenvs
           key: ${{ runner.os }}-pipenv-${{ hashFiles('**/Pipfile.lock') }}_v2
 
-      - name: Get latest commit SHA of libxc master branch
-        id: get-sha
-        run: |
-          echo "::set-output name=sha::$(git ls-remote https://github.com/ElectronicStructureLibrary/libxc.git refs/heads/master | cut -f 1)"
-        
-      - name: Cache external library
-        id: cache-libxc
-        uses: actions/cache@v3
-        with:
-          path: ~/libxc/sharedlib/
-          key: libxc-${{ runner.os }}-${{ steps.get-sha.outputs.sha }}
-
-      - name: Build and install libxc
-        if: steps.cache-libxc.outputs.cache-hit != 'true'
-        run: |
-          install_path=~/libxc/sharedlib/
-          
-          cd ~
-          git clone https://github.com/ElectronicStructureLibrary/libxc.git
-          cd ~/libxc
-          mkdir -p $install_path
-
-          cmake -H. -Bobjdir -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$install_path -DENABLE_PYTHON=ON
-          cd objdir && make
-          make test
-          make install
-
-      - name: Set LD_LIBRARY_PATH
-        run: echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/libxc/sharedlib/" >> $GITHUB_ENV
-
-      - name: Cache Python bindings
-        id: cache-bindings
-        uses: actions/cache@v3
-        with:
-          path: ~/libxc
-          key: bindings-${{ runner.os }}-${{ steps.get-libxc-sha.outputs.sha }}
-
       - name: Install dependencies
         if: steps.cache-pipenv.outputs.cache-hit != 'true'
         run: |
           cd ${{ github.workspace }}
           pipenv install --dev
 
-      - name: Install Python bindings
-        if: steps.cache-bindings.outputs.cache-hit != 'true'
-        run: |
-          pipenv run pip install ~/libxc/
-
       - name: Install atoMEC
         run: |
           cd ${{ github.workspace }}

Pipfile

@@ -9,9 +9,10 @@ scipy = ">=1.6.3"
 mendeleev = ">=0.7.0"
 tabulate = ">=0.8.9"
 joblib = ">=1.0.1"
+pylibxc = {file = "https://gitlab.com/libxc/libxc/-/archive/6.2.2/libxc-6.2.2.tar.gz"}
 
 [requires]
-python_version = "3"
+python_version = "3.12"
 
 [dev-packages]
 pytest = ">=7.1.3"

README.md

@@ -3,7 +3,7 @@
 # atoMEC: Average-Atom Code for Matter under Extreme Conditions
 
 [![docs](https://github.com/atomec-project/atoMEC/actions/workflows/gh-pages.yml/badge.svg)](https://github.com/atomec-project/atoMEC/actions/workflows/gh-pages.yml)
-[![Python 3.10](https://img.shields.io/badge/python-3.10-blue.svg)](https://www.python.org/downloads/release/python-3100/)
+[![Python 3.12](https://img.shields.io/badge/python-3.12-blue.svg)](https://www.python.org/downloads/release/python-3100/)
 [![image](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![codecov](https://codecov.io/gh/atomec-project/atoMEC/branch/develop/graph/badge.svg?token=V66CJJ3KPI)](https://codecov.io/gh/atomec-project/atoMEC)
 [![CodeFactor](https://www.codefactor.io/repository/github/atomec-project/atomec/badge)](https://www.codefactor.io/repository/github/atomec-project/atomec)
@@ -27,7 +27,17 @@ This repository is structured as follows:
 
 ## Installation
 
-Please see below sub-sections on supported operating systems and Python versions before continuing.
+The latest stable release of `atoMEC` can be installed via `pip`:
+
+`pip install atoMEC`
+
+Note that atoMEC does not (yet) support Windows installation (please see the section below on supported operating systems).
+
+The installation takes some time due to the dependence on `pylibxc`, which currently has no official wheels distribution on PyPI.
+
+Read on for instructions on how to install `atoMEC` from source, using the recommended `pipenv` installation route.
+
+### Installation via `pipenv`
 
 First, clone the atoMEC repository and ``cd`` into the main directory.
 
@@ -38,26 +48,10 @@ First, clone the atoMEC repository and ``cd`` into the main directory.
   1. First, install `pipenv` if it is not already installed, for example via `pip install pipenv` (or see [pipenv](https://pypi.org/project/pipenv/) for installation instructions)
   2. Next, install `atoMEC`'s dependencies with `pipenv install` (use `--dev` option to install the test dependencies in the same environment)
   3. Use `pipenv shell` to activate the virtual environment
-  4. Install Python bindings for `libxc`. See below section for installation instructions.
-  5. Install atoMEC with `pip install atoMEC` (for developers: `pip install -e .`)
-  6. Now run scripts from inside the `atoMEC` virtual environment, e.g. `python examples/simple.py`
-
-* Run the tests (see Testing section below) and report any failures (for example by raising an issue)
-
-### Libxc installation
-
-atoMEC relies on the [libxc](https://tddft.org/programs/libxc/) library for exchange-correlation functionals.
-
-Unfortunately, there is no official pip installation available for libxc (yet). There are two options for installation.
-
-First, ensure the virtual environment is activated (e.g. with `pipenv shell`). Then:
-
-1. Easy but **not** recommended `pip install pylibxc2`: This is an unofficial pip package for the `libxc` Python bindings. However, besides lacking official support, it does not seem to be under active maintenance. It also works only for Python <= 3.9. Nevertheless, it's an easy way to get started with atoMEC.
-2. Recommended route: Follow [official installation instructions](https://tddft.org/programs/libxc/installation/) for `libxc`'s Python bindings. Note that this requires the `cmake` build pathway with Python bindings and shared library options enabled:
-
-	`cmake -H. -Bobjdir -DBUILD_SHARED_LIBS=ON -DENABLE_PYTHON=ON`
+  4. Install atoMEC with `pip install atoMEC` (for developers: `pip install -e .`)
+  5. Now run scripts from inside the `atoMEC` virtual environment, e.g. `python examples/simple.py`
 
-Note that we provide a script `install_libxc.sh` which performs the full `libxc` installation workflow. This script has been tested on Ubuntu 22.04 and Python >= 3.8. 
+* Run the tests (see Testing section below) and report any failures (for example by raising an issue).
 
 ### Supported operating systems
 
@@ -69,8 +63,8 @@ Note that we provide a script `install_libxc.sh` which performs the full `libxc`
 
 * atoMEC has been tested and is expected to work for all Python versions >= 3.8 and <= 3.12
 * atoMEC does not work for Python <= 3.7
-* Until 09.10.2023 (release 1.4.0), all development and CI testing was done with Python 3.8. As of this date, development and CI testing is done with Python 3.10.
-* Python 3.10 is therefore the recommended version for atoMEC >= 1.4.0, since this is used for the current testing and development environment
+* Until 09.10.2023 (release 1.4.0), all development and CI testing was done with Python 3.8. As of this date, development and CI testing is done with Python 3.12.
+* Python 3.12 is therefore the recommended version for atoMEC >= 1.4.0, since this is used for the current testing and development environment
 
 
 ## Running

requirements.txt

@@ -3,3 +3,4 @@ scipy>=1.6.3
 mendeleev>=0.7.0
 tabulate>=0.8.9
 joblib>=1.0.1
+https://gitlab.com/libxc/libxc/-/archive/6.2.2/libxc-6.2.2.tar.gz

setup.py

@@ -8,23 +8,26 @@
     license = f.read()
 
 extras = {
-    'dev': ['bump2version'],
-    'docs': open('docs/requirements.txt').read().splitlines(),
-    'tests': open('tests/requirements.txt').read().splitlines(),
+    "dev": ["bump2version"],
+    "docs": open("docs/requirements.txt").read().splitlines(),
+    "tests": open("tests/requirements.txt").read().splitlines(),
 }
 
 setup(
     name="atoMEC",
     version="1.3.0",
     description="KS-DFT average-atom code",
     long_description=readme,
-    long_description_content_type='text/markdown',
+    long_description_content_type="text/markdown",
     author="Tim Callow et al.",
     author_email="t.callow@hzdr.de",
     url="https://github.com/atomec-project/atoMEC",
     license=license,
     packages=find_packages(exclude=("tests", "docs", "examples")),
-    install_requires=open('requirements.txt').read().splitlines(),
+    install_requires=open("requirements.txt").read().splitlines()[:-1],
+    dependency_links=[
+        "https://gitlab.com/libxc/libxc/-/archive/6.2.2/libxc-6.2.2.tar.gz",
+    ],
     extras_require=extras,
     python_requires=">=3.6",
 )