Merge pull request #293 from SCM-NV/restructure

MAINT, DEP: Restructure the various `qmflows` sub packages

.github/workflows/pypi.yml

@@ -8,10 +8,10 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
 
       - name: Install dependencies
         run: pip install wheel twine

.github/workflows/pythonapp.yml

@@ -5,6 +5,11 @@ on:
     branches:
       - master
   pull_request:
+  workflow_dispatch:
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+    cancel-in-progress: true
 
 jobs:
   Test:
@@ -38,12 +43,7 @@ jobs:
       CP2K_DATA_DIR: "/home/runner/work/qmflows/qmflows/cp2k/data"
 
     steps:
-    - name: Cancel Previous Runs
-      uses: styfle/cancel-workflow-action@0.9.1
-      with:
-        access_token: ${{ github.token }}
-
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     - name: Install cp2k
       if: matrix.os == 'ubuntu-latest'
@@ -53,13 +53,17 @@ jobs:
             VERSION_SHORT=$(echo "${{ matrix.special }}" | grep -P -o "CP2K \K([\.0-9]+)")
             VERSION=v"$VERSION_SHORT".0
 
+            echo ::group::"Get CP2K $VERSION data"
             git clone https://github.com/cp2k/cp2k -q
             cd cp2k
             git -c advice.detachedHead=false checkout tags/$VERSION
+            echo ::endgroup::
 
+            echo ::group::"Get CP2K $VERSION binaries"
             wget -nv https://github.com/cp2k/cp2k/releases/download/$VERSION/cp2k-$VERSION_SHORT-Linux-x86_64.ssmp -O cp2k.ssmp
             chmod u+rx cp2k.ssmp
             mv cp2k.ssmp /usr/local/bin/cp2k.popt
+            echo ::endgroup::
             ;;
           *)
             sudo apt install cp2k ;;
@@ -73,7 +77,6 @@ jobs:
       uses: s-weigand/setup-conda@v1
       with:
         update-conda: true
-        conda-channels: anaconda, conda-forge
 
     - name: Install dependencies
       shell: bash
@@ -84,7 +87,7 @@ jobs:
             source $CONDA/bin/activate test
             pip install rdkit-pypi
             pip install --pre -e .[test] --upgrade --force-reinstall
-            pip install git+https://github.com/SCM-NV/PLAMS@master --upgrade
+            pip uninstall plams -y; pip install git+https://github.com/SCM-NV/PLAMS@master --upgrade
             pip install git+https://github.com/NLeSC/noodles@master --upgrade
             ;;
           "no optional")
@@ -121,23 +124,23 @@ jobs:
             pytest -m 'not (slow or long)' ;;
         esac
 
-    - uses: codecov/codecov-action@v2
+    - uses: codecov/codecov-action@v3
       with:
         file: ./coverage.xml
         name: codecov-umbrella
 
   Linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python 3.10 on ubuntu-latest
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: "3.10"
 
       - name: Install linters
-        run: pip install pydocstyle pycodestyle mypy "numpy>=1.21" pytest more_itertools types-PyYAML types-setuptools
+        run: pip install pydocstyle pycodestyle mypy "numpy>=1.21" pytest more_itertools types-PyYAML types-setuptools "pyparsing>=3.0.8"
 
       - name: Python info
         run: |

CHANGELOG.md

@@ -114,7 +114,7 @@
 
 ## Changed
 
- * Used [pyyaml](https://pyyaml.org/wiki/PyYAMLDocumentation) for the [templates](https://github.com/SCM-NV/qmflows/blob/master/src/qmflows/templates/templates.py) instead of *JSON*
+ * Used [pyyaml](https://pyyaml.org/wiki/PyYAMLDocumentation) for the [templates](https://github.com/SCM-NV/qmflows/blob/master/src/qmflows/templates/_templates.py) instead of *JSON*
  * Updated documentation
  * Test wiht python 3.7
 

conftest.py

@@ -1,5 +1,25 @@
 """A pytest ``conftest.py`` file."""
 
 import os
+from pathlib import Path
 
-collect_ignore = [os.path.join('src', 'qmflows', 'settings.py')]
+_ROOT = Path("src") / "qmflows"
+_collect_ignore = [
+    _ROOT/ "settings.py",
+    _ROOT / "parsers" / "xyzParser.py",
+    _ROOT / "parsers" / "generic_parsers.py",
+    _ROOT / "parsers" / "parser.py",
+    _ROOT / "parsers" / "orca_parser.py",
+    _ROOT / "parsers" / "cp2KParser.py",
+    _ROOT / "parsers" / "adf_parser.py",
+    _ROOT / "templates" / "templates.py",
+    _ROOT / "packages" / "cp2k_mm.py",
+    _ROOT / "packages" / "cp2k_package.py",
+    _ROOT / "packages" / "orca.py",
+    _ROOT / "packages" / "package_wrapper.py",
+    _ROOT / "packages" / "packages.py",
+    _ROOT / "packages" / "serializer.py",
+    _ROOT / "packages" / "SCM.py",
+]
+
+collect_ignore = [str(i) for i in _collect_ignore]

docs/_packages.rst

@@ -1,11 +1,11 @@
 qmflows.packages
 ================
 
-The :class:`~qmflows.packages.packages.Package` (sub-)classes of QMFlows.
+The :class:`~qmflows.packages.Package` (sub-)classes of QMFlows.
 
 Package-related Functions
 -------------------------
-.. currentmodule:: qmflows.packages.packages
+.. currentmodule:: qmflows.packages
 .. autosummary::
     run
 
@@ -14,81 +14,111 @@ The Package Class
 .. autosummary::
     Package
     Package.__init__
-    Package.__repr__
     Package.__call__
     Package.prerun
     Package.run_job
     Package.postrun
     Package.generic2specific
     Package.handle_special_keywords
 
-Package Subclasses
-------------------
-.. currentmodule:: qmflows.packages
 .. autosummary::
-    ~SCM.ADF
-    ~SCM.DFTB
-    ~cp2k_package.CP2K
-    ~cp2k_mm.CP2KMM
-    ~orca.ORCA
-    ~package_wrapper.PackageWrapper
+    ADF
+    DFTB
+    CP2K
+    CP2KMM
+    ORCA
+    PackageWrapper
 
 Package Instances
 ------------------
 .. autosummary::
-    ~SCM.adf
-    ~SCM.dftb
-    ~cp2k_package.cp2k
-    ~cp2k_mm.cp2k_mm
-    ~orca.orca
+    adf
+    dftb
+    cp2k
+    cp2k_mm
+    orca
+
+The Result Class
+-----------------
+.. autosummary::
+    Result
+    Result.__init__
+    Result.get_property
+    Result.results
+
+.. autosummary::
+    ADF_Result
+    DFTB_Result
+    CP2K_Result
+    CP2KMM_Result
+    ORCA_Result
+    ResultWrapper
 
 API
 ---
-.. autofunction:: qmflows.packages.packages.run
+.. autofunction:: qmflows.packages.run
 
 |
 
-.. autoclass:: qmflows.packages.packages.Package
+.. autoclass:: qmflows.packages.Package
     :members: generic_mapping, result_type, pkg_name
 
-.. automethod:: qmflows.packages.packages.Package.__init__
-.. automethod:: qmflows.packages.packages.Package.__repr__
-.. automethod:: qmflows.packages.packages.Package.__call__
-.. automethod:: qmflows.packages.packages.Package.prerun
-.. automethod:: qmflows.packages.packages.Package.run_job
-.. automethod:: qmflows.packages.packages.Package.postrun
-.. automethod:: qmflows.packages.packages.Package.generic2specific
-.. automethod:: qmflows.packages.packages.Package.handle_special_keywords
+.. automethod:: qmflows.packages.Package.__init__
+.. automethod:: qmflows.packages.Package.__call__
+.. automethod:: qmflows.packages.Package.prerun
+.. automethod:: qmflows.packages.Package.run_job
+.. automethod:: qmflows.packages.Package.postrun
+.. automethod:: qmflows.packages.Package.generic2specific
+.. automethod:: qmflows.packages.Package.handle_special_keywords
 
 |
 
-.. autoclass:: qmflows.packages.SCM.ADF
+.. autoclass:: qmflows.packages.ADF
 
 |
 
-.. autoclass:: qmflows.packages.SCM.DFTB
+.. autoclass:: qmflows.packages.DFTB
 
 |
 
-.. autoclass:: qmflows.packages.cp2k_package.CP2K
+.. autoclass:: qmflows.packages.CP2K
 
 |
 
-.. autoclass:: qmflows.packages.cp2k_mm.CP2KMM
+.. autoclass:: qmflows.packages.CP2KMM
 
 |
 
-.. autoclass:: qmflows.packages.orca.ORCA
+.. autoclass:: qmflows.packages.ORCA
+
+|
+
+.. autoclass:: qmflows.packages.PackageWrapper
+    :noindex:
+
+|
+
+.. autoclass:: qmflows.packages.Result
+    :members: prop_mapping
+
+.. automethod:: qmflows.packages.Result.__init__
+.. automethod:: qmflows.packages.Result.get_property
+.. autoproperty:: qmflows.packages.Result.results
 
 |
 
-.. autoclass:: qmflows.packages.package_wrapper.PackageWrapper
+.. autoclass:: qmflows.packages.ADF_Result
+.. autoclass:: qmflows.packages.DFTB_Result
+.. autoclass:: qmflows.packages.CP2K_Result
+.. autoclass:: qmflows.packages.CP2KMM_Result
+.. autoclass:: qmflows.packages.ORCA_Result
+.. autoclass:: qmflows.packages.ResultWrapper
     :noindex:
 
 |
 
-.. autodata:: qmflows.packages.SCM.adf
-.. autodata:: qmflows.packages.SCM.dftb
-.. autodata:: qmflows.packages.cp2k_package.cp2k
-.. autodata:: qmflows.packages.cp2k_mm.cp2k_mm
-.. autodata:: qmflows.packages.orca.orca
+.. autofunction:: qmflows.packages.adf
+.. autofunction:: qmflows.packages.dftb
+.. autofunction:: qmflows.packages.cp2k
+.. autofunction:: qmflows.packages.cp2k_mm
+.. autofunction:: qmflows.packages.orca

docs/conf.py

@@ -215,5 +215,5 @@
 
 rst_epilog = """
 .. |Package| replace:: :class:`~qmflows.packages.Package`
-.. |Settings| replace:: :class:`~qmflows.settings.Settings`
+.. |Settings| replace:: :class:`~qmflows.Settings`
 """

docs/dictionaries.rst

@@ -7,4 +7,4 @@ translation of the generic keywords and properties extraction.
 
 
 to translate the generic keywords provided by the user to specific keywords used for each package.
-For instance these files are used by the :class:`~qmflows.packages.packages.Package` class.
+For instance these files are used by the :class:`~qmflows.packages.Package` class.

docs/package_wrapper.rst

@@ -1,4 +1,4 @@
 PackageWrapper
 ==============
 
-.. automodule:: qmflows.packages.package_wrapper
+.. automodule:: qmflows.packages._package_wrapper

docs/packages.rst

@@ -3,22 +3,22 @@
 Packages
 ========
 
-The base class :class:`~qmflows.packages.packages.Package` is the library core, it provides the general scaffold to call a quantum code.
+The base class :class:`~qmflows.packages.Package` is the library core, it provides the general scaffold to call a quantum code.
 On top of this infrastructure it has been created several subclasses that contain the specific details for each quantum code.
 The available interfaces to quantum codes are:
 
-* :class:`~qmflows.packages.SCM.ADF`
-* :class:`~qmflows.packages.SCM.DFTB`
-* :class:`~qmflows.packages.cp2k_package.CP2K`
-* :class:`~qmflows.packages.cp2k_mm.CP2KMM`
-* :class:`~qmflows.packages.orca.ORCA`
+* :class:`~qmflows.packages.ADF`
+* :class:`~qmflows.packages.DFTB`
+* :class:`~qmflows.packages.CP2K`
+* :class:`~qmflows.packages.CP2KMM`
+* :class:`~qmflows.packages.ORCA`
 
 
 
 **This class must not be call directly**, instead the correspoding class for the quantum package should be called or in case that there is not an interface to your quantum code,
 you can make a new subclass that implement the following method:
 
-* ``run_job`` -- This methods takes a :class:`~qmflows.settings.Settings` object a molecule and call a function to create the input automatically and takes cares of the bookkeeping associated with creating new folders, calling the package and retrieving and Object-result.
+* ``run_job`` -- This methods takes a :class:`~qmflows.Settings` object a molecule and call a function to create the input automatically and takes cares of the bookkeeping associated with creating new folders, calling the package and retrieving and Object-result.
 
 
 Instead of implementing all the runners and the bookkeeping functions ourselves, we use the plams_ library.

docs/parsers.rst

@@ -1,8 +1,8 @@
 Extracting numerical properties from output files
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Quantum packages simulations generate output file in different formats. For examples the SCM_ simulation suite
-(:class:`~qmflows.packages.SCM.ADF` and :class:`~qmflows.packages.SCM.DFTB` in *QMFlows*) generate binary outputs,
-while other packages like :class:`~qmflows.packages.cp2k_package.CP2K` and :class:`~qmflows.packages.orca.ORCA` generate ascii text files.
+(:class:`~qmflows.packages.ADF` and :class:`~qmflows.packages.DFTB` in *QMFlows*) generate binary outputs,
+while other packages like :class:`~qmflows.packages.CP2K` and :class:`~qmflows.packages.ORCA` generate ascii text files.
 
 *QMFlows* abstract away all the different commmunication protocols with the different output formats, allowing the user to
 extract the desire property by using the convention:
@@ -21,8 +21,8 @@ pacakge are implemented*. **If the property of your interest is not available yo
 
 Parsers
 ~~~~~~~
-Internally *QMFlows* uses different mechanism to extract different properties from the output files. In the case of the :class:`~qmflows.packages.SCM.ADF` and
-:class:`~qmflows.packages.SCM.DFTB` packages, *QMFlows* take advantages of the python interface to kftools_ files developed by the SCM_. In the case of *XML* output,
+Internally *QMFlows* uses different mechanism to extract different properties from the output files. In the case of the :class:`~qmflows.packages.ADF` and
+:class:`~qmflows.packages.DFTB` packages, *QMFlows* take advantages of the python interface to kftools_ files developed by the SCM_. In the case of *XML* output,
 *QMFlows* direcltly uses the python built-in xml_ reader. For the output files in text format *Qmflows* uses a mixuture of awk_ and
 *parsers*.
 

docs/promise.rst

@@ -6,9 +6,9 @@ them form an graph (specifically an acyclic direct graph) that represent these r
 
 **QMFlows** Builds the aforemention graph in order to realize the workflow evaluation order.
 For instance the figure below represent a simulation where firstly a molecular geometry optimization is carried out using the *ADF* package and
-some user defined :class:`~qmflows.settings.Settings` for the *ADF* simulation package.
+some user defined :class:`~qmflows.Settings` for the *ADF* simulation package.
 Subsequently, using the optimized molecular geometry from the previous step and
-another :class:`~qmflows.settings.Settings` for an orca simulation a job to compute the molecular frequencies is carried out.
+another :class:`~qmflows.Settings` for an orca simulation a job to compute the molecular frequencies is carried out.
 
 .. image:: _images/simple_graph.png
 
@@ -43,10 +43,10 @@ A python script corresponding with this graph can be
    >>> print(result)
 
 
-Up to the invocation of the :func:`~qmflows.packages.packages.run` function none of the computations have been executed,
-it is the :func:`~qmflows.packages.packages.run` function which builds and executes the dependencies.
+Up to the invocation of the :func:`~qmflows.packages.run` function none of the computations have been executed,
+it is the :func:`~qmflows.packages.run` function which builds and executes the dependencies.
 Since *QMFlows* needs to figure out all the dependecies in the script,
-the :func:`~qmflows.packages.packages.run` function takes as argument last dependency (or inner most dependy),
+the :func:`~qmflows.packages.run` function takes as argument last dependency (or inner most dependy),
 which in this case are the frequencies. The reason behind this, is that from the last dependency it is possible to
 retrace all the dependecies.