Merge branch 'finam_0.4_update' into 'main'

Updates for mHM v5.13.1

See merge request FINAM/finam-mhm!4

.git_archival.txt

+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

+.git_archival.txt  export-subst

.gitignore

@@ -24,6 +24,10 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
+# local version for user install
+setup.py
+# info folder with testing scirpts
+info/
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -45,6 +49,8 @@ nosetests.xml
 coverage.xml
 *.cover
 .hypothesis/
+/bench/
+/prof/
 
 # Translations
 *.mo
@@ -63,6 +69,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/source/api
 docs/output.txt
 
 # PyBuilder
@@ -88,12 +95,11 @@ celerybeat-schedule
 venv/
 ENV/
 
-# Spyder project settings
+# IDE project settings
 .spyderproject
 .spyproject
-
-# Rope project settings
 .ropeproject
+.vscode
 
 # mkdocs documentation
 /site
@@ -112,20 +118,22 @@ info/
 *.cpp
 
 # generated version file
-src/finam_mhm_module/_version.py
+src/finam_mhm/_version.py
 
 # generated docs
 docs/source/examples/
 docs/source/generated/
+examples/test_domain
+examples/qmod.nc
+examples/qmod_couple.nc
+examples/aet.nc
+examples/*.csv
+tests/runoff_out.csv
 
 /docs/build/
-/docs/finam_mhm_module.*
+/docs/finam_mhm.*
 /docs/modules.rst
-*.csv
 
 *.DS_Store
 
 *.zip
-
-# local version for user install
-setup.py

.gitlab-ci.yml

 image: python
 
 stages:
+  - test
   - build
+  - docs
   - deploy
+  - release
 
 check:
-  stage: build
+  stage: test
   before_script:
-    - apt-get install gfortran netcdf-bin libnetcdf-dev libnetcdff-dev
-    - pip3 install black numpy pandas
+    - pip3 install 'black>=23,<24' 'pylint<3' 'isort[colors]<6'
   script:
+    - pip3 install --editable .
     - black --check --diff --color .
+    - isort --check --diff --color .
+    - pylint src/finam_mhm
+
+test:
+  stage: test
+  script:
     - pip3 install --editable .[test]
-    - python -m pytest --cov finam_mhm_module --cov-report term-missing -v tests/
+    - python -m pytest --cov finam_mhm --cov-report term-missing --cov-report html:cov --cov-report xml:cov.xml -v tests/
+  coverage: '/(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'
+  artifacts:
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: cov.xml
+    paths:
+      - cov
+
+build:
+  stage: build
+  variables:
+    GIT_STRATEGY: clone
+    GIT_DEPTH: 0  # to have all tags
+  script:
+    - pip install build
+    - python -m build
+  artifacts:
+    paths:
+      - dist
+
+documentation:
+  stage: docs
+  variables:
+    GIT_STRATEGY: clone
+    GIT_DEPTH: 0  # to have all tags
+  script:
+    - pip3 install --editable .[doc]
+    - sphinx-build docs/source docs/build
+    - mv docs/build public/
+  artifacts:
+    paths:
+      - public
+
+pages:
+  stage: deploy
+  script: "true"
+  artifacts:
+    paths:
+      - public
+  only:
+    - main
+
+pypi_test_release:
+  stage: release
+  dependencies:
+    - build
+  script:
+    - pip install twine
+    - python -m twine upload --skip-existing -r testpypi -u __token__ -p ${TEST_PYPI_TOKEN} dist/*
+  artifacts:
+    paths:
+      - dist
+  only:
+    - main
+    - tags
+
+pypi_release:
+  stage: release
+  dependencies:
+    - build
+  script:
+    - pip install twine
+    - python -m twine upload -u __token__ -p ${PYPI_TOKEN} dist/*
+  artifacts:
+    paths:
+      - dist
+  only:
+    - tags

AUTHORS.md

+# FINAM-mHM developers
+
+The FINAM project was created by the following people.
+
+## Core developers
+
+- Sebastian Müller (E-mail: <sebastian.mueller@ufz.de>)
+
+## Working Group members
+
+- Jeisson Javier Leal Rojas (E-mail: <jeisson-javier.leal-rojas@ufz.de>)
+- Matthias Kelbling (E-mail: <matthias.kelbling@ufz.de>)
+
+## Supervisors
+
+- Stephan Thober (E-mail: <stephan.thober@ufz.de>)
+- Sabine Attinger (E-mail: <sabine.attinger@ufz.de>)

LICENSE.md

+# SOFTWARE LICENCE
+
+FINAM-mHM is a open-source FINAM component for mHM.
+
+## Copyright Notice
+
+Copyright © 2023, the FINAM-mHM developers from Helmholtz-Zentrum für Umweltforschung GmbH - UFZ. All rights reserved.
+
+***The code is a property of:***
+
+> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ<br/>
+> Registered Office: Leipzig<br/>
+> Registration Office: Amtsgericht Leipzig<br/>
+> Trade Register Nr. B 4703<br/>
+
+The list of FINAM-mHM developers is provided in the AUTHORS.md file.
+
+***Contact:***
+
+- FINAM Admins (E-mail: <finam@ufz.de>)
+- Sebastian Müller (E-mail: <sebastian.mueller@ufz.de>)
+- Stephan Thober (E-mail: <stephan.thober@ufz.de>)
+- Sabine Attinger (E-mail: <sabine.attinger@ufz.de>)
+
+> Department Computational Hydrosystems (CHS)<br/>
+> Helmholtz Centre for Environmental Research - UFZ<br/>
+> Permoserstr. 15<br/>
+> 04318 Leipzig, Germany
+
+This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License along with this program.
+It can be found in the files `COPYING` and `COPYING.LESSER` provided with this software.
+The complete GNU license text can also be found at < https://www.gnu.org/licenses/>.
+
+## Redistribution
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+- Redistributions of source code must retain the above copyright notice, the list of conditions for redistribution and modification as well as the following GNU Lesser General Public License.
+- Redistributions in binary form must reproduce the above copyright notice, this list of conditions, the following GNU Lesser General Public License and the modification conditions in the documentation and/or other materials provided with the distribution.
+- Neither the name of Helmholtz-Zentrum für Umweltforschung GmbH - UFZ, nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+## Modification
+
+If software is modified to produce derivative works, such modified software should be clearly marked, so as not to confuse it with the version available from Helmholtz-Zentrum für Umweltforschung GmbH - UFZ.

MANIFEST.in

-prune *
-graft src
-graft tests
-
-include LICENSE README.md pyproject.toml setup.cfg
-global-exclude __pycache__ *.py[cod] .*

README.md

 # FINAM mHM module
 
-FINAM wrapper for mHM depending on `mhm_pybind`: https://git.ufz.de/mhm/mhm_pybind
+FINAM wrapper for mHM: https://git.ufz.de/mhm/mhm
 
 ## Installation
 
 ```shell
-$ pip install git+https://git.ufz.de/FINAM/finam-mhm-module.git
+$ pip install git+https://git.ufz.de/FINAM/finam-mhm.git
 ```
+
+## License
+
+LGPLv3 (c) 2005-2023 CHS-Developers

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_static/custom.css

-
-.py.sig {
-    padding-top: 2em;
-    padding-bottom: 1em;
-}

docs/conf.py

-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-
-sys.path.insert(0, os.path.abspath("../src/finam_mhm_module"))
-
-
-# -- Project information -----------------------------------------------------
-
-project = "finam_mhm_module"
-copyright = "2022, Team LandTECH"
-author = "Team LandTECH"
-
-# The full version, including alpha/beta/rc tags
-release = "0.1.0"
-
-
-# -- General configuration ---------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = ["sphinx.ext.autodoc", "sphinx.ext.autosummary"]
-autosummary_generate = True
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ["_templates"]
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = []
-
-
-# -- Options for HTML output -------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = "alabaster"
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
-html_css_files = ["custom.css"]

docs/index.rst

-Welcome to the FINAM mHM module documentation!
-==============================================
-
-.. toctree::
-   :maxdepth: 4
-   :caption: Contents:
-
-   modules
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/_static/css/custom.css

+:root {
+  --pst-sidebar-secondary: 22rem;
+}
+html[data-theme=dark] {
+  --pst-color-primary: rgb(0, 100, 176);
+  --pst-color-link: rgb(40, 134, 204);
+}
+
+html[data-theme=light] {
+  --pst-color-primary: rgb(0, 90, 160);
+}
+
+html[data-theme=dark],
+html[data-theme=light] {
+  --pst-color-secondary: rgb(255, 166, 0);
+  --sd-color-card-border-hover: var(--pst-color-link);
+}
+
+.navbar-nav li a:focus,
+.navbar-nav li a:hover,
+.navbar-nav li.current>a,
+nav.bd-links li>a:hover {
+  color: var(--pst-color-link);
+}
+
+.blog-nav {
+	list-style: none;
+	margin-bottom: 0;
+	padding-left: 0;
+}
+
+nav.bd-links .blog-nav li>a {
+ color: var(--pst-color-text-muted);
+ display:inline;
+ padding:.25rem 0
+}
+
+ul.postlist-style-none {
+	padding-left: 0px;
+}
+
+.ablog-post-title {
+    font-size: 120%;
+}
+
+.bd-header .navbar-nav > .active > .nav-link {
+  color: var(--pst-color-link);
+}
+
+#navbar-icon-links i.fa-square-gitlab:before {
+ color: var(--pst-color-text-muted);
+}
+
+.bd-page-width {
+  max-width: 95rem;
+}
+
+.bd-page-width {
+  max-width: 95rem;
+}
+
+.center {
+  text-align: center;
+}

docs/source/_static/logo.svg

+<?xml version="1.0" encoding="UTF-8"?>
+<svg width="256" height="256" version="1.1" viewBox="0 0 256 256" xmlns="http://www.w3.org/2000/svg">
+  <g fill="#ffa600" >
+    <path d="m207.69 40-63.688 184h54.625l-8-20.281 11.266-27.719h22.109v-136z"/>
+    <path d="m57.854 224 13.772-40h88.375v40z"/>
+    <path d="m91 128 13.875-40h99.125v40z"/>
+    <path d="m208 224-8-20.281 8-19.719h24l8 40z"/>
+  </g>
+  <g fill="#005aa0">
+    <path d="m57.375 40 8 20.281-11.266 27.719h-22.109v136h16.312l63.688-184z"/>
+    <path d="m198.15 40-13.772 40h-88.375v-40z"/>
+    <path d="m165 136-13.875 40h-99.125v-40z"/>
+    <path d="m48 40 8 20.281-8 19.719h-24l-8-40z"/>
+  </g>
+  <g transform="scale(1.1,1)">
+  <text x="143" y="218" transform="skewX(-20)" fill="#005aa0" font-family="Arial" font-size="40px" font-weight="bold">
+    mHM
+  </text>
+  </g>
+</svg>

docs/source/_static/logo_large.svg

+<?xml version="1.0" encoding="UTF-8"?>
+<svg width="91" height="25" version="1.1" viewBox="0 0 91 25" xmlns="http://www.w3.org/2000/svg">
+  <g fill="#ffa600">
+    <path d="m6.2317 24 1.7214-5h11.047v5z"/>
+    <path d="m10.375 12 1.7344-5h12.391v5z"/>
+    <path d="m24.961 1-7.9609 23h6.8281l-1-2.5352 1.4082-3.4648h2.7637v-17z"/>
+    <path d="m25 24-1-2.5351 1-2.4649h3l1 5z"/>
+  </g>
+  <g fill="#005aa0">
+    <path d="m 6.1719,1 1,2.5352 L 5.7637,7 H 3 V 24 H 5.0391 L 13,1 Z"/>
+    <path d="m23.768 1-1.7214 5h-11.047v-5z"/>
+    <path d="m19.625 13-1.7344 5h-12.391v-5z"/>
+    <path d="M 5,1 6,3.5351 5,6 H 2 L 1,1 Z"/>
+  </g>
+  <text x="30" y="15" fill="#005aa0" font-family="Arial" font-size="19.6px" font-weight="bold">
+    FINAM
+  </text>
+  <text x="30.75" y="24" fill="#ffa600" font-family="Arial" font-size="7.3px" font-weight="bold">
+    mHM Component
+  </text>
+</svg>

docs/source/_templates/autosummary/class.rst

+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :undoc-members:
+   :inherited-members:
+   :show-inheritance:
+
+.. raw:: latex
+
+    \clearpage

docs/source/_templates/autosummary/module.rst

+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ fullname }}
+
+.. automodule:: {{ fullname }}
+
+.. raw:: latex
+
+    \clearpage