Merge de355de into d174eb4

.pre-commit-config.yaml

@@ -1,36 +1,54 @@
 # Install pre-commit hooks via
 # pre-commit install
 
-# modernizer: make sure our code-base is Python 3 ready
-#- repo: https://github.com/python-modernize/python-modernize.git
-#  sha: a234ce4e185cf77a55632888f1811d83b4ad9ef2
-#  hooks:
-#  - id: python-modernize
-#    exclude: ^docs/
-#    args:
-#      - --write
-#      - --nobackups
+- 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:
-  # yapf = yet another python formatter
+
   - id: yapf
-    name: yapf
+    name: Yet Another Python Formatter
     entry: yapf
     language: system
-    exclude: '^(aiida_crystal17/tests/)'
-
-  # prospector: collection of linters
-  - id: prospector
-    language: system
-    types: [file, python]
-    name: prospector
-    description: "This hook runs Prospector: https://github.com/landscapeio/prospector"
-    entry: prospector
-    exclude: '^(aiida_crystal17/tests/)|(examples/)'
+    types: [python]
+    args: ["-i", "-vv"]
 
   - id: version-number
     name: Check version numbers
-    entry: python ./.travis-data/check_version.py
+    entry: python ./.travis-data/check_version.py version
     language: system
-    files: '^(setup.json)|(aiida_crystal17/__init__.py)'
+    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|
+        environment.yml|
+      )$
+    pass_filenames: false
+
+  - id: travis-linter
+    name: Travis Lint
+    entry: travis lint
+    files: .travis.yml
+    language: ruby
+    additional_dependencies: ['travis']

.travis-data/check_version.py

@@ -1,34 +1,107 @@
-"""Check that version numbers match.
+"""Validate consistency of versions and dependencies.
 
-Check version number in setup.json and aiida_crystal17/__init__.py and make sure
-they match.
+Validates consistency of setup.json and
+
+ * environment.yml
+ * version in aiida/__init__.py
 """
-import os
 import json
+import os
 import sys
 
-this_path = os.path.split(os.path.realpath(__file__))[0]
-
-# Get content of setup.json
-setup_fname = 'setup.json'
-setup_path = os.path.join(this_path, os.pardir, setup_fname)
-with open(setup_path) as f:
-    setup_content = json.load(f)
-
-# Get version from python package
-sys.path.insert(0, os.path.join(this_path, os.pardir))
-import aiida_crystal17  # noqa
-version = aiida_crystal17.__version__
-
-if version != setup_content['version']:
-    print("Version number mismatch detected:")
-    print("Version number in '{}': {}".format(setup_fname,
-                                              setup_content['version']))
-    print("Version number in '{}/__init__.py': {}".format(
-        'aiida_crystal17', version))
-    sys.exit(1)
-
-# Overwrite version in setup.json
-# setup_content['version'] = version
-# with open(setup_path, 'w') as f:
-# 	json.dump(setup_content, f, indent=4, sort_keys=True)
+import click
+
+FILENAME_SETUP_JSON = 'setup.json'
+SCRIPT_PATH = os.path.split(os.path.realpath(__file__))[0]
+ROOT_DIR = os.path.join(SCRIPT_PATH, os.pardir)
+FILEPATH_SETUP_JSON = os.path.join(ROOT_DIR, FILENAME_SETUP_JSON)
+
+
+def get_setup_json():
+    """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)
+
+    return setup_json
+
+
+@click.group()
+def cli():
+    pass
+
+
+@cli.command('version')
+def validate_version():
+    """Check that version numbers match.
+
+    Check version number in setup.json and aiida_crystal17/__init__.py and make sure
+    they match.
+    """
+    # Get version from python package
+    sys.path.insert(0, ROOT_DIR)
+    import aiida_crystal17  # pylint: disable=wrong-import-position
+    version = aiida_crystal17.__version__
+
+    setup_content = get_setup_json()
+    if version != setup_content['version']:
+        click.echo('Version number mismatch detected:')
+        click.echo("Version number in '{}': {}".format(FILENAME_SETUP_JSON, setup_content['version']))
+        click.echo("Version number in '{}/__init__.py': {}".format('aiida_crystal17', version))
+        click.echo("Updating version in '{}' to: {}".format(FILENAME_SETUP_JSON, version))
+
+        setup_content['version'] = version
+        with open(FILEPATH_SETUP_JSON, 'w') as fil:
+            # Write with indentation of two spaces and explicitly define separators to not have spaces at end of lines
+            json.dump(setup_content, fil, indent=2, separators=(',', ': '))
+
+        sys.exit(1)
+
+
+@cli.command('conda')
+def update_environment_yml():
+    """
+    Updates environment.yml file for conda.
+    """
+    import re
+    from ruamel.yaml.comments import CommentedMap, CommentedSeq
+    from ruamel.yaml import YAML
+
+    cmap = CommentedMap()
+    cmap.yaml_set_start_comment('Usage: conda env create -n myenvname -f environment.yml python=3.6')
+    cmap['name'] = 'aiida_crystal17'
+    cmap['channels'] = CommentedSeq(['conda-forge', 'cjs'])
+    cmap['channels'].yaml_add_eol_comment('for sqlalchemy-diff and pgtest', 1)
+    cmap['dependencies'] = dmap = CommentedSeq()
+
+    # fix incompatibilities between conda and pypi
+    replacements = {}
+    setup_json = get_setup_json()
+
+    for base, key in [(None, 'install_requires'), ('extras_require', 'testing'), ('extras_require', 'code_style'),
+                      ('extras_require', 'docs')]:
+        requirements = setup_json.get(base, setup_json)[key]
+        count = 0
+        for req in sorted(requirements, key=lambda x: x.lower()):
+            # skip packages required for specific python versions < 3
+            if re.findall("python_version\\s*\\<\\s*\\'?3", req):
+                continue
+            req = req.split(';')[0]
+            for (regex, replacement) in iter(replacements.items()):
+                req = re.sub(regex, replacement, req)
+            count += 1
+            dmap.append(req.lower())
+
+        dmap.yaml_set_comment_before_after_key(len(dmap) - count, before=key)
+
+    yaml = YAML(typ='rt')
+    yaml.default_flow_style = False
+    yaml.encoding = 'utf-8'
+    yaml.allow_unicode = True
+    environment_filename = 'environment.yml'
+    file_path = os.path.join(ROOT_DIR, environment_filename)
+    with open(file_path, 'w') as env_file:
+        yaml.dump(cmap, env_file)
+
+
+if __name__ == '__main__':
+    cli()  # pylint: disable=no-value-for-parameter

.travis.yml

@@ -33,6 +33,10 @@ matrix:
 install:
 # Upgrade pip setuptools and wheel
 - pip install -U "pip<19" wheel setuptools "reentry>=1.3"
+- |
+    if [[ "$TEST_TYPE" == "version" ]]; then
+      pip install click
+    fi
 - |
     if [[ "$TEST_TYPE" == "code-style" ]]; then
       pip install "flake8<3.8.0,>=3.7.0"
@@ -85,7 +89,7 @@ script:
   fi
 - |
   if [[ "$TEST_TYPE" == "version" ]]; then
-    python ./.travis-data/check_version.py
+    python ./.travis-data/check_version.py version
   fi
 
 after_success:

.vscode/settings.json

@@ -14,7 +14,7 @@
         "**/.eggs": true
     },
 
-    "python.pythonPath": "/anaconda/envs/aiida-workshop/bin/python",
+    "python.pythonPath": "/anaconda/envs/aiida_crystal17/bin/python",
     "python.formatting.provider": "yapf",
     "python.linting.pylintEnabled": false,
     "python.linting.flake8Enabled": true,