Release v0.10.0b5, merge PR #27 from chrisjsewell/develop

.condarc

@@ -7,4 +7,4 @@ channels:
 show_channel_urls: True
 
 # For more information about this file see:
-# https://conda.io/docs/user-guide/configuration/use-condarc.html
+# https://conda.io/docs/user-guide/configuration/use-condarc.html

.coveragerc

@@ -2,5 +2,3 @@
 
 
 [report]
-
-

.flake8

@@ -1,2 +1,5 @@
 [flake8]
-max-line-length = 121
+max-line-length = 121
+import-order-style = appnexus
+application-import-names = aiida_crystal17
+application-package-names = aiida

.gitchangelog.rc

@@ -94,6 +94,13 @@ ignore_regexps = [
     r'^([cC]hg|[fF]ix|[nN]ew)\s*:\s*[d|D]ev:',
     r'^(.{3,3}\s*:)?\s*[fF]irst commit.?\s*$',
     r'^$',  # ignore commits with empty messages
+
+    # one time removals
+    r'^[Pp]re commit( test)? fix\.$',
+    r'^Add test for aiida development version.*$',
+    r'^Test correction\.$',
+    r'^Minor improvements\.$',
+    r'^Style test fix\.$',
 ]
 
 # ``section_regexps`` is a list of 2-tuples associating a string label and a

.pre-commit-config.yaml

@@ -1,60 +1,70 @@
 # Install pre-commit hooks via
 # pre-commit install
 
-- repo: git://github.com/pre-commit/pre-commit-hooks
-  sha: v2.2.3
-  hooks:
-  - id: check-json
-  - id: check-yaml
-  - id: end-of-file-fixer
-  - id: trailing-whitespace
-  - id: double-quote-string-fixer
-  - id: flake8
-
-- repo: local
-  hooks:
-
-  - id: yapf
-    name: Yet Another Python Formatter
-    entry: yapf
-    language: system
-    types: [python]
-    args: ["-i", "-vv"]
-
-  - id: version-number
-    name: Check version numbers
-    entry: python ./.travis-data/check_version.py version
-    language: system
-    files: >-
-      (?x)^(
-        setup.json|
-        .travis-data/check_version.py|
-        aiida_crystal17/__init__.py
-      )$
-    pass_filenames: false
-
-  - id: conda
-    name: Create environment.yml
-    entry: python ./.travis-data/check_version.py conda
-    language: system
-    files: >-
-      (?x)^(
-        setup.json|
-        setup.py|
-        .travis-data/check_version.py|
-        conda_dev_env.yml|
-      )$
-    pass_filenames: false
-
-  - id: travis-linter
-    name: Travis Lint
-    entry: travis lint
-    files: .travis.yml
-    language: ruby
-    additional_dependencies: ['travis']
-
-  - id: doc8
-    entry: doc8
-    language: system
-    types: [rst]
-    name: doc8 - Lint the documentation.
+exclude: >
+  (?x)^(
+      aiida_crystal17/tests/raw_files/.*|
+      cry17_scripts/.*
+  )$
+
+repos:
+
+  - repo: git://github.com/pre-commit/pre-commit-hooks
+    rev: v2.2.3
+    hooks:
+    - id: check-json
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+    - id: double-quote-string-fixer
+    - id: flake8
+
+  - repo: local
+    hooks:
+
+    - id: yapf
+      name: Yet Another Python Formatter
+      entry: yapf
+      language: system
+      types: [python]
+      args: ["-i", "-vv"]
+
+    - id: version-number
+      name: Check version numbers
+      entry: python ./.pre-commit/check_version.py version
+      language: system
+      files: >-
+        (?x)^(
+          setup.json|
+          .pre-commit/check_version.py|
+          aiida_crystal17/__init__.py
+        )$
+      pass_filenames: false
+
+    - id: conda
+      name: Create environment.yml
+      entry: python ./.pre-commit/check_version.py conda
+      language: system
+      files: >-
+        (?x)^(
+          setup.json|
+          setup.py|
+          .pre-commit/check_version.py|
+          conda_dev_env.yml|
+        )$
+      pass_filenames: false
+
+    - id: travis-linter
+      name: Travis Lint
+      entry: travis lint
+      files: .travis.yml
+      language: ruby
+      additional_dependencies: ['travis']
+
+    - id: doc8
+      entry: doc8
+      language: system
+      types: [rst]
+      name: doc8 - Lint the documentation.
+
+    # TODO could also add check-manifest

.travis-data/check_version.py → .pre-commit/check_version.py

@@ -18,7 +18,7 @@
 
 
 def get_setup_json():
-    """Return the `setup.json` as a python dictionary """
+    """Return the `setup.json` as a python dictionary."""
     with open(FILEPATH_SETUP_JSON, 'r') as handle:
         setup_json = json.load(handle)  # , object_pairs_hook=OrderedDict)
 
@@ -27,6 +27,7 @@ def get_setup_json():
 
 @click.group()
 def cli():
+    """Command line interface for pre-commit checks."""
     pass
 
 
@@ -59,9 +60,7 @@ def validate_version():
 
 @cli.command('conda')
 def update_environment_yml():
-    """
-    Updates conda_dev_env.yml file for conda.
-    """
+    """Update conda_dev_env.yml file for conda."""
     import re
     from ruamel.yaml.comments import CommentedMap, CommentedSeq
     from ruamel.yaml import YAML

.readthedocs.yml

@@ -16,4 +16,3 @@ python:
 #   builder: html
 #   configuration: conf.py
 #   fail_on_warning: true
-

.style.yapf

@@ -1,3 +1,4 @@
 [style]
 based_on_style = google
-column_limit = 120
+column_limit = 120
+indent_dictionary_value = true

.travis.yml

@@ -16,48 +16,61 @@ addons:
 matrix:
   include:
     - python: 3.6
-      env: TEST_TYPE="code-style"
+      env: TEST_TYPE="pre-commit"
     - python: 3.6
-      env: TEST_TYPE="version"
-    - python: 3.6
-      env: TEST_TYPE="pytest" TEST_AIIDA_BACKEND="django" MOCK_CRY17_EXECUTABLES=true PYPI_DEPLOY=true
+      env: TEST_TYPE="pytest" TEST_AIIDA_BACKEND="django" PYPI_DEPLOY=true
     - python: 2.7
-      env: TEST_TYPE="pytest" TEST_AIIDA_BACKEND="django" MOCK_CRY17_EXECUTABLES=true
+      env: TEST_TYPE="pytest" TEST_AIIDA_BACKEND="django"
     - python: 3.6
-      env: TEST_TYPE="pytest" TEST_AIIDA_BACKEND="sqlalchemy" MOCK_CRY17_EXECUTABLES=true
+      env: TEST_TYPE="pytest" TEST_AIIDA_BACKEND="sqlalchemy"
     - python: 3.6
       env: TEST_TYPE="docs" READTHEDOCS="True"
+    - python: 3.6
+      env: TEST_TYPE="conda"
 
   # allow_failures:
   #   - env: TEST_TYPE="docs" READTHEDOCS="True"
 
 install:
 # Upgrade pip setuptools and wheel
-- pip install -U "pip<19" wheel setuptools "reentry>=1.3"
+- pip install --upgrade pip wheel setuptools "reentry>=1.3"
+- pip install numpy==1.16.4 # otherwise numpy 1.17 is installed, which is incompatible with aiida-core==1.0.0b5
 - |
-    if [[ "$TEST_TYPE" == "version" ]]; then
-      pip install click
+    if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      pip install typing==3.6.6 # otherwise importlib_resources installs incompatible version for aiida-core==1.0.0b5
     fi
 - |
-    if [[ "$TEST_TYPE" == "code-style" ]]; then
-      pip install "flake8<3.8.0,>=3.7.0"
+    if [[ "$TEST_TYPE" == "pre-commit" ]]; then
+      pip install -e .[code_style]
     fi
 - |
     if [[ "$TEST_TYPE" == "pytest" ]]; then
-      pip uninstall -y numpy
+      pip install "notebook<5.5"  # required by aiida-core->circus->pyzmq<17
       pip install -e .[testing]
       pip install coveralls
     fi
 - |
     if [[ "$TEST_TYPE" == "docs" ]]; then
-      pip uninstall -y numpy
       pip install -e .[docs]
       url="https://github.com/jgm/pandoc/releases/tag/2.6"
       path=$(curl -L $url | grep -o '/jgm/pandoc/releases/download/.*-amd64\.deb')
       downloadUrl="https://github.com$path"
       file=${path##*/}
       wget $downloadUrl && sudo dpkg -i $file
     fi
+- |
+    if [[ "$TEST_TYPE" == "conda" ]]; then
+      # See https://conda.io/docs/user-guide/tasks/use-conda-with-travis-ci.html#the-travis-yml-file
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+      bash miniconda.sh -b -p $HOME/miniconda
+      export PATH="$HOME/miniconda/bin:$PATH"
+      hash -r
+      conda config --set always_yes yes --set changeps1 no
+      conda update -q conda
+      # Useful for debugging any issues with conda
+      conda info -a
+    fi
+
 # - |
 #   if [[ ! -z "${AIIDA_BRANCH}" ]]; then
 #     cur_path="$(pwd)"
@@ -80,21 +93,29 @@ script:
       pytest -v --cov=aiida_crystal17 --cov=examples --cov-config .coveragerc --cov-report= aiida_crystal17
   fi
 - |
-  if [[ "$TEST_TYPE" == "code-style" ]]; then
-    flake8 .
+  if [[ "$TEST_TYPE" == "pre-commit" ]]; then
+    pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
   fi
 - |
   if [[ "$TEST_TYPE" == "docs" ]]; then
     cd docs
     make
   fi
 - |
-  if [[ "$TEST_TYPE" == "version" ]]; then
-    python ./.travis-data/check_version.py version
+  if [[ "$TEST_TYPE" == "conda" ]]; then
+    travis_retry conda env create -f conda_dev_env.yml -n test-environment python=$TRAVIS_PYTHON_VERSION
+    conda list -n test-environment
+    source activate test-environment
+    pip install --no-deps -e .
+    reentry scan
+    verdi data crystal17.parse --help
   fi
 
 after_success:
-- coveralls
+- |
+  if [[ "$TEST_TYPE" == "pytest" ]]; then
+      coveralls
+  fi
 
 deploy:
   - provider: pypi

.vscode/settings.json

@@ -29,13 +29,14 @@
     "restructuredtext.confPath": "${workspaceFolder}/docs/source",
     "restructuredtext.linter.extraArgs": ["--max-line-length", "120"],
     "cSpell.words": [
-        "aiida"
+        "aiida",
+        "pytest"
     ],
-    "todo-tree.tags": [
+    "todo-tree.general.tags": [
         "TODO",
         "todo::",
         "FIXME",
         "NOTE"
-      ],
-    "todo-tree.regex": "((//|#-?|<!--|\\.\\.|;|/\\*|^)\\s*($TAGS)|^\\s*- \\[ \\])"
+    ],
+    "todo-tree.regex.regex": "((//|#-?|<!--|\\.\\.|;|/\\*|^)\\s*($TAGS)|^\\s*- \\[ \\])"
 }

MANIFEST.in

@@ -1,4 +1,5 @@
 include LICENSE
+include pyproject.toml
 include setup.json
 recursive-include aiida_crystal17/tests/raw_files *
-include aiida_crystal17/validation/*.json
+include aiida_crystal17/validation/schemas/*.json