Merge pull request #174 from JuDFTteam/release-0.11.0

🚀 Release `0.11.0`
JuDFTteam · Jun 27, 2022 · 2f97cd3 · 2f97cd3
2 parents 20c0628 + 96b5593
commit 2f97cd3
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diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
@@ -17,14 +17,14 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3.1.2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4.0.0
       with:
-        python-version: 3.9
+        python-version: '3.10'
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         path: ~/.cache/pip
         key: pip-docs-${{ hashFiles('**/pyproject.toml') }}
@@ -68,15 +68,15 @@ jobs:
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         path: ~/.cache/pip
         key: pip-pre-commit-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-pre-commit-
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3.1.2
+      uses: actions/setup-python@v4.0.0
       with:
         python-version: 3.8
 
@@ -104,15 +104,15 @@ jobs:
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         path: ~/.cache/pip
         key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-${{ matrix.python-version }}-tests
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3.1.2
+      uses: actions/setup-python@v4.0.0
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -130,7 +130,7 @@ jobs:
         pip install codecov
         codecov
 
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       if: failure()
       with:
         name: matplotlib-comparison-${{ matrix.python-version }}
@@ -144,7 +144,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python 3.7
-        uses: actions/setup-python@v3.1.2
+        uses: actions/setup-python@v4.0.0
         with:
           python-version: 3.7
       - name: Install flit

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -11,14 +11,14 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3.1.2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4.0.0
       with:
-        python-version: 3.9
+        python-version: '3.10'
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         path: ~/.cache/pip
         key: pip-docs-${{ hashFiles('**/pyproject.toml') }}
@@ -62,15 +62,15 @@ jobs:
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         path: ~/.cache/pip
         key: pip-pre-commit-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-pre-commit-
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3.1.2
+      uses: actions/setup-python@v4.0.0
       with:
         python-version: 3.8
 
@@ -103,15 +103,15 @@ jobs:
 
     - name: Cache python dependencies
       id: cache-pip
-      uses: actions/[email protected].2
+      uses: actions/[email protected].4
       with:
         path: ~/.cache/pip
         key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/pyproject.toml') }}
         restore-keys: |
           pip-${{ matrix.python-version }}-tests
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3.1.2
+      uses: actions/setup-python@v4.0.0
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -129,7 +129,7 @@ jobs:
         pip install codecov
         codecov
 
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       if: failure()
       with:
         name: matplotlib-comparison-${{ matrix.python-version }}

diff --git a/.github/workflows/fleur-release.yml b/.github/workflows/fleur-release.yml
@@ -14,7 +14,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3.1.2
+      uses: actions/setup-python@v4.0.0
       with:
         python-version: 3.8
 
@@ -40,7 +40,7 @@ jobs:
       run: exit 1
 
     - name: Create Pull Request
-      uses: peter-evans/[email protected].2
+      uses: peter-evans/[email protected].4
       with:
         commit-message: "[fleur release] Fleur schema update"
         branch: fleur-release/schema

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,7 +5,7 @@ ci:
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.2.0
     hooks:
     - id: double-quote-string-fixer
       types: [python]
@@ -42,7 +42,7 @@ repos:
       ]
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.1
+    rev: v2.32.0
     hooks:
     -   id: pyupgrade
         args: [
@@ -52,6 +52,13 @@ repos:
 - repo: local
   hooks:
 
+  #Since this runs after the formatter the docstrings should already satisfy all other hooks
+  - id: make-fleurxmlmodifier-doc
+    name: Generate Docstrings for Setter methods of FleurXMLModifier
+    entry: python ./utils/write_fleurxmlmodifier_docstrings.py
+    language: system
+    pass_filenames: false
+
   - id: pylint-errors
     name: pylint-errors
     entry: pylint
@@ -103,4 +110,5 @@ repos:
             masci_tools/tools/greensfunction.py|
             masci_tools/cmdline/parameters/slice.py|
             masci_tools/vis/parameters.py|
+            masci_tools/util/ipython.py|
         )$
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,12 +5,13 @@ formats:
   - pdf
 
 python:
-  version: 3.9
   install:
     - method: pip
       path: .
       extra_requirements:
         - docs
 
 build:
-  image: testing
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,53 @@
 # Changelog
 
+## v.0.11.0
+[full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.10.1...v0.11.0)
+
+This release adds some improvements to the XML and HDF5 handling mainly for better AiiDA-Fleur
+support. Also major updates to documentation configurations and Green's function calculations.
+
+### Added
+- Added `FleurElementMaker` class. This can be used to create XML elements compatible with a given version from scratch.
+  Has case-insensitivity and converts values to strings for XML [[#159]](https://github.com/JuDFTteam/masci-tools/pull/159)
+  Example
+  ```python
+   from masci_tools.util.xml.builder import FleurElementMaker
+   E = FleurElementMaker.fromVersion('0.35')
+   new_kpointset = E.kpointlist(
+       *(
+           E.kpoint(kpoint, weight=weight, label=special_labels[indx]) if indx in special_labels else
+           E.kpoint(kpoint, weight=weight) for indx, (kpoint, weight) in enumerate(zip(kpoints, weights))
+       ),
+       name=name,
+       count=nkpts,
+       type=kpoint_type)
+  ```
+- Function `serialize_xml_arguments` to `masci_tools.util.xml.common_functions` to remove XML elements/trees from positional/keyword arguments and replace them with string representations of the XML. Can be used in AiiDA-Fleur
+- Module `masci_tools.util.ipython` and ipython extension (`%load_ext masci_tools`). Adds syntax highlighted XML tree output and creating HTML syntax highlighted diffs of XML trees [[#158]](https://github.com/JuDFTteam/masci-tools/pull/158)
+- Added calculation of Jij Tensor from intersite Green's functions [[#170]](https://github.com/JuDFTteam/masci-tools/pull/170)
+
+### Improvements
+- Added `name` entry to `SchemaDict.tag_info` which contains the tag name in the original case [[#159]](https://github.com/JuDFTteam/masci-tools/pull/159)
+- `convert_to_xml` is made more strict. Conversion `int` to `str` uses the `{:d}` format specifier and string conversion is no longer always attempted [[#159]](https://github.com/JuDFTteam/masci-tools/pull/159)
+- Improvements to Colorbar creation in matplotlib plotting methods. Limits are now set consistently with `limits={'color': (low, high)}` in the plot and colorbar. Spinpolarized bandplots now show two colorbars for the two colormaps if requested
+- `get_parameter_data` now also extracts the `gamma` switch for kpoint generation for more consistent roundtrips. This is only set if the first kpoint in the mesh is the gamma point and there are multiple
+- `load_inpxml` and `load_outxml` now consistently accept the XML file given as a
+string of the content. The content no longer has to be manually encoded as bytes
+- The method `FleurXMLModifier.modify_xmlfile` now always returns two things. The modified XML tree and a dictionary with all additional file contents, e.g. `n_mmp_mat`.
+- Support for aligning spin/real-space frames of Green's functions. Several further imporvements/bugfixes for Green's function modules [[#170]](https://github.com/JuDFTteam/masci-tools/pull/170)
+
+### Bugfixes
+- Bugfix for `outxml_parser` returning a nested list for Hubbard 1 distances, where a flat list was expected. Removed `force_list` argument from the parsing task definition
+- Fixes in `plot_fleur_bands`, when providing custom weights without spin suffixes, i.e. `_up`/`_down`
+- Fix in `HDF5Reader`. IO like objects without an attached filename would lead to an  early error. This is the case for example for some readers in the file repository implementation used in AiiDA v2.0
+- Fix in `HDF5Reader`. The file handles for compressed files in the AiiDA v2 repository have to be copied into a temporary file first before they can be used
+
+### For Developers
+- Docs: Updated `sphinx` and `sphinx-autodoc-typehints` versions and build docs on python 3.10 [[#156]](https://github.com/JuDFTteam/masci-tools/pull/156)
+- Docs: Converted to `MyST` markdown and where appropriate introduced `myst-nb` for executing code cells in the documentation, e.g. generate plotting examples [[#157]](https://github.com/JuDFTteam/masci-tools/pull/157)
+- Bokeh regression tests now strip out the bokeh version from the test files
+- Added pre-commit hook, which generates the docstrings for the `FleurXMLModifier` registration methods from their XML setter function counterparts [[#166]](https://github.com/JuDFTteam/masci-tools/pull/166)
+
 ## v0.10.1
 [full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.10.0...v0.10.1)
 
@@ -13,11 +61,11 @@ This release provides several new features in the XML modification/evaluation fo
 working with DFT+U density matrix files are also fixed.
 ### Added
 - New XML setter `align_nmmpmat_to_sqa` to rotate the density matrix file according to SQAs specified either for noco or second variation SOC [[#140]](https://github.com/JuDFTteam/masci-tools/pull/140)
-- Added `task_list` property to `FleurXMLModifier` to construct a list which can be used to replicate the same `FleurXMLModifier` with the `fromList()` classmethod [[#149]](https://github.com/JuDFTteam/masci-tools/pull/#149)
-- Added `FleurXMLContext`, which acts as a holder of th XML elements,  schema dictionary, constants and logger to reduce the amount of information/clutter in functions evaluating things from the XML file [[#152]](https://github.com/JuDFTteam/masci-tools/pull/#152)
+- Added `task_list` property to `FleurXMLModifier` to construct a list which can be used to replicate the same `FleurXMLModifier` with the `fromList()` classmethod [[#149]](https://github.com/JuDFTteam/masci-tools/pull/149)
+- Added `FleurXMLContext`, which acts as a holder of th XML elements,  schema dictionary, constants and logger to reduce the amount of information/clutter in functions evaluating things from the XML file [[#152]](https://github.com/JuDFTteam/masci-tools/pull/152)
 
   Note: The class `ParseTasks` used in the `outxml_parser` was simplified and placed into the `outxml_parser` module and the decorator `register_parsing_function` was removed. This was done without deprecation since they were exclusively used in the `outxml_parser` and were the main cause of cyclic import problems previously
-- Added several predefined conversions to/from input version `0.35` to `inpxml_converter` [[#153]](https://github.com/JuDFTteam/masci-tools/pull/#153)
+- Added several predefined conversions to/from input version `0.35` to `inpxml_converter` [[#153]](https://github.com/JuDFTteam/masci-tools/pull/153)
 
 ### Improvements
 - Added `inverse` argument to nmmpmat XML setters. These will correctly produce the inverse rotation operation for the given angles. Also allow setting `orbital='all'` in `rotate_nmmpmat` to rotate all blocks by the given angles [[#140]](https://github.com/JuDFTteam/masci-tools/pull/140)
@@ -28,11 +76,11 @@ working with DFT+U density matrix files are also fixed.
 - Added basic tests of `masci_tools.tools.greensfunction` module and fixed several bugs found due to this [[#150]](https://github.com/JuDFTteam/masci-tools/pull/150)
 - Fixed bug in XML setters operating on the DFT+U density matrix file not correctly extracting the number of spin blocks when only setting `l_mperp`
 - Fixed bug, when using the `FleurXMLModifier` directly (not in `aiida-fleur`), included XML files were not handled
-- Fixed bug in `outxml_parser`, when the XML file had to be repaired and more than one iteration was present the wrong iteration was chosen as the last stable iteration [[#152]](https://github.com/JuDFTteam/masci-tools/pull/#152)
+- Fixed bug in `outxml_parser`, when the XML file had to be repaired and more than one iteration was present the wrong iteration was chosen as the last stable iteration [[#152]](https://github.com/JuDFTteam/masci-tools/pull/152)
 
 ### Deprecated
-- The module `masci_tools.io.io_fleurxml` is renamed to `masci_tools.io.fleur_xml` [[#152]](https://github.com/JuDFTteam/masci-tools/pull/#152)
-- The module `masci_tools.util.parse_task_decorator` is removed. All decorators are now availaibe under `masci_tools.io.parsers.fleur` [[#152]](https://github.com/JuDFTteam/masci-tools/pull/#152)
+- The module `masci_tools.io.io_fleurxml` is renamed to `masci_tools.io.fleur_xml` [[#152]](https://github.com/JuDFTteam/masci-tools/pull/152)
+- The module `masci_tools.util.parse_task_decorator` is removed. All decorators are now availaibe under `masci_tools.io.parsers.fleur` [[#152]](https://github.com/JuDFTteam/masci-tools/pull/152)
 
 ### For Developers
 - Added `py.typed` marker to masci-tools, since a large part of the outside facing code (especially the XML APIs are typed). With this marker other packages can use the typehints in this package

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -27,7 +27,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['myst_parser',
+extensions = ['myst_nb',
               'sphinx.ext.autodoc',
               'sphinx.ext.doctest',
               'sphinx.ext.todo',
@@ -36,17 +36,20 @@
               'sphinx.ext.ifconfig',
               'sphinx.ext.viewcode',
               'sphinx.ext.intersphinx',
-              'sphinx_toolbox.more_autodoc.typehints',
-              'sphinx_toolbox.more_autodoc.overloads',
               'sphinx_autodoc_typehints',
+              'sphinx_copybutton',
               'sphinx_click']
 
 intersphinx_mapping = {'numpy': ('https://numpy.org/doc/stable/', None),
                        'python': ('https://docs.python.org/3', None),
                        'lxml': ('https://lxml.de/apidoc/',None),
-                       'h5py': ('https://docs.h5py.org/en/latest/', None)}
+                       'h5py': ('https://docs.h5py.org/en/latest/', None),
+                       'pandas': ('http://pandas.pydata.org/pandas-docs/dev', None)}
 
-myst_enable_extensions = []
+myst_enable_extensions = ['colon_fence',
+                          'fieldlist',
+                          'dollarmath',
+                          'deflist']
 
 todo_include_todos = True
 
@@ -255,7 +258,7 @@
         # No sphinx_rtd_theme installed
         pass
 
-autodoc_mock_imports = ['bokeh']
+autodoc_mock_imports = ['bokeh', '_typeshed']
 
 
 # -- Options for manual page output ---------------------------------------
@@ -397,15 +400,10 @@
     ('py:obj', 'plum'),
     ('py:class', 'etree._XPathObject'),
     ('py:class', 'h5py._hl.group.Group'),
-    ('py:class', 'etree._Element'),
-    ('py:class', 'etree.XPath'),
     ('py:class', 'TypeAlias'),
-    ('py:class', 'Logger'),
-    ('py:class', 'FilterType'),
-    ('py:class', 'XMLLike'),
-    ('py:class', 'etree.XPathElementEvaluator'),
     ('py:class', 'contextlib._GeneratorContextManager'),
-    ('py:data', 'masci_tools.io.parsers.fleur.fleur_outxml_parser.F')
+    ('py:data', 'masci_tools.io.parsers.fleur.fleur_outxml_parser.F'),
+    ('py:class', 'np.ndarray')
 ]