Reset project in preparation of re-write (#42)

.devcontainer/Dockerfile

@@ -0,0 +1,5 @@
+FROM --platform=linux/x86_64 condaforge/mambaforge:latest
+
+RUN    apt update                               \
+    && apt install -y git make build-essentials \
+    && rm -rf /var/lib/apt/lists/*

.devcontainer/devcontainer.json

@@ -0,0 +1,4 @@
+{
+  "build": { "dockerfile": "Dockerfile" },
+  "postCreateCommand": "make env"
+}

.github/workflows/ci.yaml

@@ -1,62 +1,32 @@
 name: CI
 
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
 on:
-  push:
-    branches:
-      - "main"
-  pull_request:
-    branches:
-      - "main"
-  schedule:
-    - cron: "0 0 * * *"
+  push: { branches: [ "main" ] }
+  pull_request: { branches: [ "main" ] }
 
 jobs:
   test:
 
-    name: ${{ matrix.os }} python=${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest]
-        python-version: [3.7]
+    runs-on: ubuntu-latest
+    container: condaforge/mambaforge:latest
 
     steps:
-    - uses: actions/checkout@v2.3.4
-
-    - name: Setup Conda Environment
-      uses: conda-incubator/setup-miniconda@v2.1.1
-      with:
-        python-version: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/meta.yaml
-
-        channels: conda-forge,defaults
-
-        activate-environment: test
-        auto-update-conda: true
-        auto-activate-base: false
-        show-channel-urls: true
-
-    - name: Install Package
-      shell: bash -l {0}
-      run: |
-        python setup.py develop --no-deps
-
-    - name: Conda Environment Information
-      shell: bash -l {0}
-      run: |
-        conda info
-        conda list
+    - uses: actions/checkout@v3.3.0
 
     - name: Run Tests
-      shell: bash -l {0}
       run: |
-        pytest -v --cov=descent --cov-report=xml --color=yes descent/tests/
+        apt update && apt install -y git make
+        
+        make env
+        make lint
+        make test
 
     - name: CodeCov
-      uses: codecov/codecov-action@v2.0.3
+      uses: codecov/codecov-action@v3.1.1
       with:
         file: ./coverage.xml
         flags: unittests
-        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}

.gitignore

@@ -105,8 +105,11 @@ ENV/
 # There are reports this comes from LLVM profiling, but also Xcode 9.
 *profraw
 
+# PyCharm
+.idea
+
 # OSX
-*DS_Store
+.DS_Store
 
-# PyCharm
-.idea
+# Local development
+scratch

.pre-commit-config.yaml

@@ -0,0 +1,38 @@
+repos:
+  - repo: local
+    hooks:
+      - id: isort
+        name: "[Package] Import formatting"
+        language: system
+        entry: isort
+        files: \.py$
+
+      - id: black
+        name: "[Package] Code formatting"
+        language: system
+        entry: black
+        files: \.py$
+
+      - id: flake8
+        name: "[Package] Linting"
+        language: system
+        entry: flake8
+        files: \.py$
+
+      - id: isort-examples
+        name: "[Examples] Import formatting"
+        language: system
+        entry: nbqa isort
+        files: examples/.+\.ipynb$
+
+      - id: black-examples
+        name: "[Examples] Code formatting"
+        language: system
+        entry: nbqa black
+        files: examples/.+\.ipynb$
+
+      - id: flake8-examples
+        name: "[Examples] Linting"
+        language: system
+        entry: nbqa flake8 --ignore=E402
+        files: examples/.+\.ipynb$

LICENSE

@@ -1,7 +1,7 @@
 
 MIT License
 
-Copyright (c) 2021 Simon Boothroyd
+Copyright (c) 2023 Simon Boothroyd
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Makefile

@@ -0,0 +1,32 @@
+PACKAGE_NAME  := descent
+CONDA_ENV_RUN := conda run --no-capture-output --name $(PACKAGE_NAME)
+
+.PHONY: pip-install env lint format test test-examples
+
+pip-install:
+	$(CONDA_ENV_RUN) pip install --no-build-isolation --no-deps -e .
+
+env:
+	mamba create     --name $(PACKAGE_NAME)
+	mamba env update --name $(PACKAGE_NAME) --file devtools/envs/base.yaml
+	$(CONDA_ENV_RUN) pip install --no-build-isolation --no-deps -e .
+	$(CONDA_ENV_RUN) pre-commit install || true
+
+lint:
+	$(CONDA_ENV_RUN) isort --check-only $(PACKAGE_NAME)
+	$(CONDA_ENV_RUN) black --check      $(PACKAGE_NAME)
+	$(CONDA_ENV_RUN) flake8             $(PACKAGE_NAME)
+	$(CONDA_ENV_RUN) nbqa isort   --check-only  examples
+	$(CONDA_ENV_RUN) nbqa black   --check       examples
+	$(CONDA_ENV_RUN) nbqa flake8  --ignore=E402 examples
+
+format:
+	$(CONDA_ENV_RUN) isort  $(PACKAGE_NAME)
+	$(CONDA_ENV_RUN) black  $(PACKAGE_NAME)
+	$(CONDA_ENV_RUN) flake8 $(PACKAGE_NAME)
+	$(CONDA_ENV_RUN) nbqa isort                examples
+	$(CONDA_ENV_RUN) nbqa black                examples
+	$(CONDA_ENV_RUN) nbqa flake8 --ignore=E402 examples
+
+test:
+	$(CONDA_ENV_RUN) pytest -v --cov=$(PACKAGE_NAME) --cov-report=xml --color=yes $(PACKAGE_NAME)/tests/

descent/__init__.py

@@ -1,12 +1,10 @@
 """
-DESCENT
+descent
 
-Optimize force field parameters against QC data using `pytorch`
+Optimize classical force field parameters against reference data
 """
 
-from ._version import get_versions
+from . import _version
 
-versions = get_versions()
-__version__ = versions["version"]
-__git_revision__ = versions["full-revisionid"]
-del get_versions, versions
+__version__ = _version.get_versions()["version"]
+__all__ = ["__version__"]