Release v1.5.0 (#47)

* Main back to develop (#45)

* added ecp functionality

* add macos folders to gitignore

* more options for setting basis

* ecp tests and updates

* fix linting

* add raises regex match

* update flake8

* fix pre-commit and linting

* more linting

* fix fmt parameter to comply with pymatgen new convention

* Updated version and documentation for 1.3.1 release.

* Update version of isort in .pre-commit-config

This is to solve an issue with poetry config that is used in isort.

* Update pyproject.toml

Changed requirement on pymatgen version.

* Update pyproject.toml

Updated monty's dependency

* Fixed comparison in test_files.

* Fixed comparison utility function for tests.

* Linting.

* Fixed import error of plotting function from pymatgen for py3.9+.

* Updated docs html.

* Update version in pyproject.toml (#42)

* added ecp functionality

* add macos folders to gitignore

* more options for setting basis

* ecp tests and updates

* fix linting

* add raises regex match

* update flake8

* fix pre-commit and linting

* more linting

* fix fmt parameter to comply with pymatgen new convention

* Merge main back into develop (#41)

* added ecp functionality

* add macos folders to gitignore

* more options for setting basis

* ecp tests and updates

* fix linting

* add raises regex match

* update flake8

* fix pre-commit and linting

* more linting

* fix fmt parameter to comply with pymatgen new convention

* Updated version and documentation for 1.3.1 release.

* Update version of isort in .pre-commit-config

This is to solve an issue with poetry config that is used in isort.

* Update pyproject.toml

Changed requirement on pymatgen version.

* Update pyproject.toml

Updated monty's dependency

* Fixed comparison in test_files.

* Fixed comparison utility function for tests.

* Linting.

* Fixed import error of plotting function from pymatgen for py3.9+.

* Updated docs html.

---------

Co-authored-by: Will Laderer <[email protected]>
Co-authored-by: Guido Petretto <[email protected]>

* Update version in pyproject.

---------

Co-authored-by: Will Laderer <[email protected]>
Co-authored-by: Guido Petretto <[email protected]>

---------

Co-authored-by: Will Laderer <[email protected]>
Co-authored-by: Guido Petretto <[email protected]>

* Updates for TM 7.7.1 + big refactoring (#46)

* updates for supporting TM v7.6

* fix linting

* Updated version and documentation for 1.3.1 release.

* Update version of isort in .pre-commit-config

This is to solve an issue with poetry config that is used in isort.

* Update pyproject.toml

Changed requirement on pymatgen version.

* Update pyproject.toml

Updated monty's dependency

* Fixed comparison in test_files.

* Fixed comparison utility function for tests.

* Linting.

* Fixed import error of plotting function from pymatgen for py3.9+.

* Updated docs html.

* Added tests_config.yaml and TMV6 in list of tests to be performed.

* Updated docs and version.

* Fixed aoforce parsing in TM 7.7.

* Fixed reading of coord file with "natoms= ..." in first line.
Fixed test that now fails when running define with frozen cartesian
coordinates + frozen internal coordinates.

* Fixed parsing of irrep_data for TM>=7.7.

* Fixed escf parsing.

* Updated reference files for integration tests.

* Fixed is_uhf parsing method.

* Generated new reference files for unit tests.

* Updated html docs and version.

* Updated checkout and setup-python actions in CI.

* Big refactoring of turbomoleio.
Switched to src layout.
Extracted out tests from src directory and moved tests to tests
directory.
Several other small modifications.

* Updated changelog.

* Removed python 3.8 from tests.

* Trying to fix issue on CI with TEST_DATA defined in code instead of
tests.

* Fixing test_data in CI.

* Fixing test_data in CI.

* Fixing test_data in CI

* Fixing version from src code in docs_rst/conf.py.
Adding unit tests.

* Linting tests.

* Adding unit tests.

* Added unit tests for control.py

* Adding unit tests.

* Adding unit tests.

* Adding unit tests.

* Adding unit tests.

* Adding unit tests.

* Added unit tests.

* Added no branch.

* Adding unit tests.

* Adding unit tests.

* Adding unit tests.

* Adding unit tests.

* Add fail_under = 100 for coverage.

* Adding unit tests.

* Fixed addopts for pytest.

* Adding unit tests.

* Modified pytest execution in github ci workflow.

* Adding unit tests.

* Trying to fix pytest ci coverage options.

* Unit tests + trying to fix pytest's CI workflow.

* Trying to fix pytest ci ...

* Trying to fix gh ci.

* Trying to fix gh ci wf file.

* Fixed available_templates to be returned as alphabetical

* Adding unit tests.

* Adding unit tests.

* Adding unit tests.

* Adding no branch.

* Adding unit tests.

* Adding no branch.

* Adding unit tests for run_itest.

* Moving imports upwards + small change in run_itest.

* Adding unit tests.

* Added references for run_itest.

* Fixes + updates of reference files.

* Fixed zip strict for python 3.9.

* Added no cover for dryrun and generation in run_itest.

* Added unit tests.
Reached 100% coverage for unit tests.
When using no cover, usually a small explanation of why it is disabled
for coverage is provided.
For testing the testing framework (in particular, the run_itest
function), nothing is tested on dryrun or generation capabilities.

* Added unit test to get 100% coverage in py3.9.

* Updates following GP's review.

* Updated release date + updated documentation.

---------

Co-authored-by: Guido Petretto <[email protected]>

---------

Co-authored-by: Will Laderer <[email protected]>
Co-authored-by: Guido Petretto <[email protected]>

.github/workflows/main_ci.yml

@@ -11,11 +11,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: '3.9'
       - name: Linting
         run: |
           pip install pre-commit
@@ -27,28 +27,23 @@ jobs:
     strategy:
       max-parallel: 2
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11']
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: pyproject.toml
 
-      - name: Get full python version
-        id: full-python-version
-        shell: bash
-        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
-      - name: Install pytest
-        shell: bash
-        run: pip install pytest
-
-      - name: Install turbomoleio
-        shell: bash
-        run: pip install .
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[dev]
 
       - name: Run pytest
         shell: bash
-        run: pytest -m 'not integration'
+        run: pytest --cov=turbomoleio --cov-report=xml -m "not integration"
+#        run: pytest -m 'not integration'

dev_scripts/generate_output_files.py

@@ -35,6 +35,7 @@
 import os
 import shutil
 import sys
+from pathlib import Path
 
 from monty.os import cd, makedirs_p
 from monty.serialization import dumpfn, loadfn
@@ -45,17 +46,20 @@
 from turbomoleio.input.utils import get_define_template
 from turbomoleio.output.files import EscfOnlyOutput, JobexOutput, exec_to_out_obj
 from turbomoleio.output.parser import Parser
-from turbomoleio.testfiles.utils import (
+from turbomoleio.testing import (
     PARSER_METHODS,
-    TESTDIR,
     TM_VERSIONS,
     compare_differences,
     generate_control_for_test,
     generate_reference_output,
 )
 
-gen_dir = os.path.join(TESTDIR, "outputs", "generation")
-OUTPUTS_BASENAMES = loadfn(os.path.join(gen_dir, "tests_config.yaml"))["testlist"]
+module_dir = Path(__file__).resolve().parent.parent
+TEST_DATA = module_dir / "tests" / "test_data"
+TEST_DATA = TEST_DATA.resolve()
+
+gen_dir = TEST_DATA / "outputs" / "generation"
+OUTPUTS_BASENAMES = loadfn(gen_dir / "tests_config.yaml")["testlist"]
 exec_to_out_obj = dict(exec_to_out_obj)
 exec_to_out_obj["jobex"] = JobexOutput
 
@@ -247,8 +251,8 @@ def get_version_dir(version_dir, force, compare_to):
     print(f"Turbomole version {tm_version} detected")
     if not version_dir:
         version_dir = f"TM_v{tm_version}"
-    vdir_path = os.path.join(TESTDIR, "outputs", version_dir)
-    if not force and os.path.exists(vdir_path):
+    vdir_path = TEST_DATA / "outputs" / version_dir
+    if not force and vdir_path.exists():
         print(
             "Directory exists. If generation of existing tests is performed, "
             "code will exit. Use --force to overwrite."
@@ -259,10 +263,10 @@ def get_version_dir(version_dir, force, compare_to):
         f"<testfiles/outputs/{version_dir}>."
     )
     if compare_to is None:
-        ref_vdir_path = os.path.join(TESTDIR, "outputs", TM_VERSIONS[-1])
+        ref_vdir_path = TEST_DATA / "outputs" / TM_VERSIONS[-1]
     else:
-        ref_vdir_path = os.path.join(TESTDIR, "outputs", compare_to)
-    if not os.path.exists(ref_vdir_path):
+        ref_vdir_path = TEST_DATA / "outputs" / compare_to
+    if not ref_vdir_path.exists():
         print("Reference version directory does not exist")
         exit()
     return vdir_path, ref_vdir_path
@@ -641,7 +645,7 @@ def update_json_files(dryrun, rtol, atol, print_diffs):
     """
     print("Updating json files")
     for tm_version in TM_VERSIONS:
-        vdir_path = os.path.join(TESTDIR, "outputs", tm_version)
+        vdir_path = os.path.join(TEST_DATA, "outputs", tm_version)
         vdir_testlist = loadfn(os.path.join(vdir_path, "tests_config.yaml"))["testlist"]
         version_all_diffs = {}
         for tm_exec, testnames in vdir_testlist.items():

docs/_modules/index.html

@@ -1,9 +1,9 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; turbomoleio 1.4.0 documentation</title>
+  <title>Overview: module code &mdash; turbomoleio 1.5.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
 
@@ -14,9 +14,9 @@
 
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=b308ce55"></script>
+        <script src="../_static/documentation_options.js?v=e0a75244"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
-        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
@@ -34,7 +34,7 @@
             turbomoleio
           </a>
               <div class="version">
-                1.4.0
+                1.5.0
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -97,25 +97,14 @@ <h1>All modules for which code is available</h1>
 <li><a href="turbomoleio/core/datagroups.html">turbomoleio.core.datagroups</a></li>
 <li><a href="turbomoleio/core/molecule.html">turbomoleio.core.molecule</a></li>
 <li><a href="turbomoleio/core/periodic.html">turbomoleio.core.periodic</a></li>
-<li><a href="turbomoleio/core/tests/test_control.html">turbomoleio.core.tests.test_control</a></li>
-<li><a href="turbomoleio/core/tests/test_datagroups.html">turbomoleio.core.tests.test_datagroups</a></li>
-<li><a href="turbomoleio/core/tests/test_molecule.html">turbomoleio.core.tests.test_molecule</a></li>
-<li><a href="turbomoleio/core/tests/test_periodic.html">turbomoleio.core.tests.test_periodic</a></li>
-<li><a href="turbomoleio/core/tests/test_utils.html">turbomoleio.core.tests.test_utils</a></li>
 <li><a href="turbomoleio/core/utils.html">turbomoleio.core.utils</a></li>
 <li><a href="turbomoleio/input/define.html">turbomoleio.input.define</a></li>
-<li><a href="turbomoleio/input/tests/test_define.html">turbomoleio.input.tests.test_define</a></li>
-<li><a href="turbomoleio/input/tests/test_utils.html">turbomoleio.input.tests.test_utils</a></li>
+<li><a href="turbomoleio/input/templates.html">turbomoleio.input.templates</a></li>
 <li><a href="turbomoleio/input/utils.html">turbomoleio.input.utils</a></li>
 <li><a href="turbomoleio/output/data.html">turbomoleio.output.data</a></li>
 <li><a href="turbomoleio/output/files.html">turbomoleio.output.files</a></li>
 <li><a href="turbomoleio/output/parser.html">turbomoleio.output.parser</a></li>
 <li><a href="turbomoleio/output/states.html">turbomoleio.output.states</a></li>
-<li><a href="turbomoleio/output/tests/test_data.html">turbomoleio.output.tests.test_data</a></li>
-<li><a href="turbomoleio/output/tests/test_files.html">turbomoleio.output.tests.test_files</a></li>
-<li><a href="turbomoleio/output/tests/test_parser.html">turbomoleio.output.tests.test_parser</a></li>
-<li><a href="turbomoleio/output/tests/test_states.html">turbomoleio.output.tests.test_states</a></li>
-<li><a href="turbomoleio/testfiles/utils.html">turbomoleio.testfiles.utils</a></li>
 </ul>
 
            </div>