Merge branch 'develop' of github.com:addman2/aiida_python into develop

.github/workflows/ci.yml

@@ -0,0 +1,58 @@
+name: Build and test
+
+on: [push, pull_request]
+
+jobs:
+
+  build-and-test:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Setup python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Setup RabbitMQ
+        uses: nijel/rabbitmq-action@v1.0.0
+        with:
+          rabbitmq version: 3.8.9
+
+      - name: Install code
+        run: |
+          pip install .[testing,pre-commit]
+
+      - name: Test code
+        run: |
+          pytest -s .
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Setup python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Setup RabbitMQ
+        uses: nijel/rabbitmq-action@v1.0.0
+        with:
+          rabbitmq version: 3.8.9
+
+      - name: Install code
+        run: |
+          pip install .[pre-commit]
+
+      - name: Run pre-commit
+        run: |
+          pre-commit install
+          pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

.github/workflows/pypi_publish.yml

@@ -0,0 +1,39 @@
+name: Publish on PyPI
+
+on:
+  push:
+    tags:
+      # After vMajor.Minor.Patch _anything_ is allowed (without "/") !
+      - v[0-9]+.[0-9]+.[0-9]+*
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    if: github.repository == 'addman2/aiida-python' && startsWith(github.ref, 'refs/tags/v')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/aiida-python
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+
+    - name: Upgrade setuptools and install package
+      run: |
+        python -m pip install --upgrade pip setuptools build wheel
+        python -m pip install -e .
+
+    - name: Build source distribution
+      run: python -m build --sdist --bdist_wheel --outdir dist/ .
+
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+# Install pre-commit hooks via:
+# pre-commit install
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v3.4.0
+  hooks:
+    - id: double-quote-string-fixer
+    - id: end-of-file-fixer
+    - id: fix-encoding-pragma
+    - id: mixed-line-ending
+    - id: trailing-whitespace
+    - id: check-json
+
+# yapf = yet another python formatter
+- repo: https://github.com/pre-commit/mirrors-yapf
+  rev: v0.30.0
+  hooks:
+  - id: yapf
+    name: yapf
+    args: ["-i"]
+
+    #- repo: local
+    #hooks:
+
+#  - id: version-number
+#    name: Check version numbers
+#    entry: python ./.github/check_version.py
+#    language: system
+#    files: '^(setup.json)|(qp2/__init__.py)'

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+python:
+   install:
+     - requirements: docs/source/requirements.txt

MANIFEST.in

@@ -0,0 +1,2 @@
+include setup.json
+include LICENCE

README.md

@@ -1,12 +1,12 @@
 # AiiDA Python
 
-This package allows you to run python code as `CalcJob` on a remote computer. Usage is easy one has to inherit CalcJobPython class and instead of `prepare_for_submition` method one ahs to overload `run_python`. Parser is generated automatically one does not have to write its own.
+This package is an AiiDA plugin allowing you to run python code as `CalcJob` on a remote computer. Usage is easy one has to inherit CalcJobPython class and instead of `prepare_for_submition` method one ahs to overload `run_python`. Parser is generated automatically one does not have to write its own.
 
 
 ```from aiida.orm import (Int, Float, Str, List, ArrayData)
 from aiida.plugins import CalculationFactory
 
-CalcJobPython = CalculationFactory("aiida_python.calc")
+CalcJobPython = CalculationFactory("python.calc")
 
 class ClassThatCannotStartWithTestExample(CalcJobPython):
 
@@ -58,4 +58,4 @@ def test_example(aiida_local_code_factory, clear_database):
     result = run(calculation, **inputs)
 ```
 
-THIS IS IN TESTING STAGE
+For more information look at this [link](https://aiida-python.readthedocs.io/en/latest/).

aiida_python/__init__.py

@@ -1 +1,4 @@
+# -*- coding: utf-8 -*-
 from .serializers import *
+
+__version__ = '0.0.6'

aiida_python/calc.py

@@ -2,23 +2,21 @@
 
 from aiida.common import datastructures
 from aiida.engine import CalcJob
-from aiida.orm import (Data,
-                       Int,
-                       Float,
-                       Str)
+from aiida.orm import (Data, Int, Float, Str)
+
+INFILE = '.__data_mia.inpkl'
+OUTFILE = '.__data_mia.outpkl'
+ERRFILE = '.__data_mia.errpkl'
 
-INFILE = ".__data_mia.inpkl"
-OUTFILE = ".__data_mia.outpkl"
-ERRFILE = ".__data_mia.errpkl"
 
 class NoRunPythonMethod(Exception):
     pass
 
+
 class CalcJobPython(CalcJob):
     """
     AiiDA Python calculation class
     """
-
     @classmethod
     def define(cls, spec):
         super().define(spec)
@@ -33,51 +31,66 @@ def define(cls, spec):
                    required=False,
                    help='Dont leave this empty')
 
-        spec.inputs['metadata']['options']['parser_name'].default = 'aiida_python.parser'
-        spec.inputs['metadata']['options']['input_filename'].default = '__noone_will_ever_use_this_name.input'
-        spec.inputs['metadata']['options']['output_filename'].default = '__noone_will_ever_use_this_name.output'
-
-        spec.inputs['metadata']['options']['serializers'].default = ['int',
-                                                                     'float',
-                                                                     'str',
-                                                                     'list',
-                                                                     'arraydata',]
-        spec.output('run_code',
-                    valid_type=Str,
-                    help='Code that had been run')
+        spec.inputs['metadata']['options'][
+            'parser_name'].default = 'python.parser'
+        spec.inputs['metadata']['options'][
+            'input_filename'].default = '__noone_will_ever_use_this_name.input'
+        spec.inputs['metadata']['options'][
+            'output_filename'].default = '__noone_will_ever_use_this_name.output'
+
+        spec.inputs['metadata']['options']['serializers'].default = [
+            'int',
+            'float',
+            'str',
+            'list',
+            'arraydata',
+        ]
+        spec.output('run_code', valid_type=Str, help='Code that had been run')
 
         spec.output('error_message',
                     valid_type=Str,
                     help='Error message if exception was raised')
 
-        spec.exit_code(300, 'ERROR_MISSING_OUTPUT_VARIABLES', message='Calculation did not produce all expected output files.')
+        spec.exit_code(
+            300,
+            'ERROR_MISSING_OUTPUT_VARIABLES',
+            message='Calculation did not produce all expected output files.')
 
     def serialize(self, fhandle):
         """
         """
 
-        import pkg_resources
+        from aiida.plugins import entry_point as ep
+
         def serialize_this(obj):
-            for entry_point in pkg_resources.iter_entry_points('aiida_python.serializers'):
-                if entry_point.name in self.inputs['metadata']['options']['serializers']:
+            for entry_point in ep.eps().select(
+                    group='aiida_python.serializers'):
+                if entry_point.name in self.inputs['metadata']['options'][
+                        'serializers']:
                     obj = entry_point.load().serialize(obj)
             return obj
 
         """
         o linja mute mute ...
         """
-        data = { inp: serialize_this(self.inputs[inp]) for inp in self.inputs if inp not in ('metadata', 'code') }
+        data = {
+            inp: serialize_this(self.inputs[inp])
+            for inp in self.inputs if inp not in ('metadata', 'code')
+        }
         """
         fixme: Make a warning if something was not serialized
         """
-        data = { key: val for key, val in data.items() if not isinstance(val, Data) }
+        data = {
+            key: val
+            for key, val in data.items() if not isinstance(val, Data)
+        }
 
         import pickle
         pickle.dump(data, fhandle)
 
     def prepare_for_submission(self, folder):
 
-        run_python = getattr(self, "run_python", None)
+        run_python = getattr(self, 'run_python', None)
         if not callable(run_python):
             # None type is not callable, right?
             raise NoRunPythonMethod()
@@ -100,19 +113,19 @@ def prepare_for_submission(self, folder):
         """
 
         #source_code = [ l[4:-1] for l in source_code ]
-        source_code = ['import os',
-                       'os.system("mkdir ihyh")',
-                       'os.system("echo \'from .ihyh import IHideYouHolder\' > ihyh/__init__.py")',
-                       'os.system("cp ihyh.py ihyh")',
-                       'from ihyh import IHideYouHolder'] + source_code
+        source_code = [
+            'import os', 'os.system("mkdir ihyh")',
+            'os.system("echo \'from .ihyh import IHideYouHolder\' > ihyh/__init__.py")',
+            'os.system("cp ihyh.py ihyh")', 'from ihyh import IHideYouHolder',
+        ] + source_code
 
         arguments = f'infile="{INFILE}", outfile="{OUTFILE}"'
-        runline = f"run_python(IHideYouHolder({arguments}))"
-        trailing_code = ['try:',
-                         f'    {runline}',
-                         'except Exception as exc:',
-                         f'    with open("{ERRFILE}", "w") as fhandle:',
-                         '        fhandle.write(str(exc))']
+        runline = f'run_python(IHideYouHolder({arguments}))'
+        trailing_code = [
+            'try:', f'    {runline}', 'except Exception as exc:',
+            f'    with open("{ERRFILE}", "w") as fhandle:',
+            '        fhandle.write(str(exc))'
+        ]
         #source_code.append(f'try:\n    run_python(IHideYouHolder({arguments}))\nexcept:\n    os.system("echo ijo ike > {ERRFILE}")')
         source_code = '\n'.join(source_code + trailing_code)
 
@@ -126,7 +139,8 @@ def prepare_for_submission(self, folder):
              open(ihyh_file, 'r') as fhandle_source:
             fhandle_destination.write(fhandle_source.read())
 
-        with folder.open(self.inputs.metadata.options.input_filename, "w") as fhandle:
+        with folder.open(self.inputs.metadata.options.input_filename,
+                         'w') as fhandle:
             fhandle.write(source_code)
 
         with folder.open(INFILE, 'wb') as fhandle:
@@ -142,13 +156,14 @@ def prepare_for_submission(self, folder):
         calcinfo.codes_info = [codeinfo]
         calcinfo.local_copy_list = []
 
-        calcinfo.retrieve_list = [self.inputs.metadata.options.output_filename,
-                                  self.inputs.metadata.options.input_filename,
-                                  OUTFILE,
-                                  ERRFILE,
-                                 ]
-        if "retrieve_list" in self.helper:
-            calcinfo.retrieve_list.extend(self.helper["retrieve_list"])
+        calcinfo.retrieve_list = [
+            self.inputs.metadata.options.output_filename,
+            self.inputs.metadata.options.input_filename,
+            OUTFILE,
+            ERRFILE,
+        ]
+        if 'retrieve_list' in self.helper:
+            calcinfo.retrieve_list.extend(self.helper['retrieve_list'])
 
         return calcinfo
 
@@ -159,26 +174,24 @@ def _process_docs(self, folder, docs):
         import re
         import os
 
-        for line in docs.split("\n"):
+        for line in docs.split('\n'):
             m = re.match(r'.*!file\s+(.+):\s*([_a-zA-Z0-9]+)\s*$', line)
             if m:
                 self._op_file_in(folder, m.group(1), m.group(2))
                 self._op_file_out(folder, m.group(2))
 
     def _op_file_out(self, folder, filename):
-        if "retrieve_list" not in self.helper:
+        if 'retrieve_list' not in self.helper:
             self.helper['retrieve_list'] = []
         self.helper['retrieve_list'].append(filename)
 
     def _op_file_in(self, folder, inputname, filename):
         try:
-            with folder.open(filename, "wb") as fhandle_destination, \
-                 getattr(self.inputs, inputname).open(mode="rb") as fhandle_source:
+            with folder.open(filename, 'wb') as fhandle_destination, \
+                 getattr(self.inputs, inputname).open(mode='rb') as fhandle_source:
                 fhandle_destination.write(fhandle_source.read())
         except AttributeError:
             """
             If input port does not exists do nothing
             """
             pass
-
-

aiida_python/data/__init__.py

@@ -1 +1,2 @@
+# -*- coding: utf-8 -*-
 from .ihyh import IHideYouHolder