🚀 Prepare 0.4.0 release (#709)

* 🩹 Fixed old/broken link to docs * ⬆️ Removed '.dev' from __version__ Note for tests to work locally you need to reinstall pyglotaran (pip install -e .) * 👌 Changed HISTORY.rst to changelog.md and added myst-parser For the docs to build locally you ned to install the updated requirements (pip install -r docs/requirements.txt) * 👌 Updated changelog * Polish up for 0.4.0 release Upgraded Development Status to Beta Standardized Glotaran and pyglotaran spelling - GloTarAn (*Glo*bal *Tar*get *An*alysis) -> Glotaran - pyGloTarAn -> pyglotaran - pyglotaran_examples -> pyglotaran-examples (the repo) Clean up references on Authors page Changed URLs from http to https where possible Moved some notes on robust covarience matrix calculation to PR #706 Co-authored-by: Joris Snellenburg <jsnel@users.noreply.github.com>
glotaran · Jun 25, 2021 · dc00e6d · dc00e6d
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diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -22,6 +22,6 @@ Supervision
 
 Original publications
 ---------------------
-1. Snellenburg JJ, Laptenok SP, Seger R, Mullen KM, van Stokkum IHM (2012). “Glotaran: A Java-Based Graphical User Interface for the R Package TIMP.” Journal of Statistical Software, 49(3), 1–22. URL http://www.jstatsoft.org/v49/i03/.
-2. Mullen, Katharine, & Ivo H. M. van Stokkum. "TIMP: An R Package for Modeling Multi-way Spectroscopic Measurements." Journal of Statistical Software [Online], 18.3 (2007): 1 - 46. Web. 25 Jul. URL https://www.jstatsoft.org/article/view/v018i03
-3. van Stokkum, IHM, Delmar S. Larsen, and Rienk van Grondelle. "Global and target analysis of time-resolved spectra." Biochimica et Biophysica Acta (BBA)-Bioenergetics 1657.2-3 (2004): 82-104. https://doi.org/10.1016/j.bbabio.2004.04.011
+1. Joris J. Snellenburg, Sergey Laptenok, Ralf Seger, Katharine M. Mullen, Ivo H. M. van Stokkum. "Glotaran: A Java-Based Graphical User Interface for the R Package TIMP". Journal of Statistical Software (2012), Volume 49, Number 3, Pages: 1–22. URL https://dx.doi.org/10.18637/jss.v049.i03
+2. Katharine M. Mullen, Ivo H. M. van Stokkum. "TIMP: An R Package for Modeling Multi-way Spectroscopic Measurements". Journal of Statistical Software (2007), Volume 18, Number 3, Pages 1-46, ISSN 1548-7660. URL https://dx.doi.org/10.18637/jss.v018.i03
+3. Ivo H. M. van Stokkum, Delmar S. Larsen, Rienk van Grondelle, "Global and target analysis of time-resolved spectra". Biochimica et Biophysica Acta (BBA) - Bioenergetics (2004), Volume 1657, Issues 2–3, Pages 82-104, ISSN 0005-2728. URL https://doi.org/10.1016/j.bbabio.2004.04.011
diff --git a/HISTORY.rst b/HISTORY.rst
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
-# pyGloTarAn
+# pyglotaran
 
-pyGloTarAn is a Python library for Global and Target Analysis
+pyglotaran is a Python library for Global and Target Analysis
 
 [![latest release](https://pypip.in/version/pyglotaran/badge.svg)](https://pypi.org/project/pyglotaran/)
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/pyglotaran.svg)](https://anaconda.org/conda-forge/pyglotaran)
@@ -16,7 +16,7 @@ pyGloTarAn is a Python library for Global and Target Analysis
 
 Prerequisites:
 
-- Python 3.8 (Python 3.9 is only supported as of v0.3.3)
+- Python 3.8 or 3.9
 - On Windows only 64bit is supported
 
 Note for Windows Users: The easiest way to get python for Windows is via [Anaconda](https://www.anaconda.com/)
@@ -55,13 +55,13 @@ This software package is made available as an early access release, to the advan
 
 Anyone using this package for serious work - scientists and academic users in particular - are cautioned, and treat it as any other instrument or tool that requires calibration or validation. Also be prepared for some refactoring of models or analysis specifications, sometime down the line.
 
-As of yet, the pyglotaran package has not yet been used in any peer-reviewed scientific publications (contribution welcome), but it has been partially cross-validated against comparable software, such as the [R-package TIMP](http://dx.doi.org/10.18637/jss.v018.i03), and the TIM software described in [this publication](https://doi.org/10.1016/j.bbabio.2004.04.011) ([DOI: 10.1016/j.bbabio.2004.04.011](https://doi.org/10.1016/j.bbabio.2004.04.011)).
+As of yet, the pyglotaran package has not yet been used in any peer-reviewed scientific publications (contribution welcome), but it has been partially cross-validated against comparable software, such as the [R-package TIMP](https://dx.doi.org/10.18637/jss.v018.i03), and the TIM software described in [this publication](https://doi.org/10.1016/j.bbabio.2004.04.011) ([DOI: 10.1016/j.bbabio.2004.04.011](https://doi.org/10.1016/j.bbabio.2004.04.011)).
 
-The examples used in this validation process can be obtained from the [pyglotaran_examples repository](https://github.com/glotaran/pyglotaran_examples).
+The examples used in this validation process can be obtained from the [pyglotaran-examples repository](https://github.com/glotaran/pyglotaran-examples).
 
 ## Glotaran legacy
 
-The pyglotaran package derives its name from the glotaran software package (now called [glotaran-legacy](https://github.com/glotaran/glotaran-legacy)), first released in 2011 and described in a highly-cited publication in the Journal of Statistical Software, under the title [Glotaran: A Java-Based Graphical User Interface for the R Package TIMP](https://www.jstatsoft.org/article/view/v049i03) ([DOI: 10.18637/jss.v049.i03](http://dx.doi.org/10.18637/jss.v049.i03)).
+The pyglotaran package derives its name from the Glotaran software package (now called [glotaran-legacy](https://github.com/glotaran/glotaran-legacy)), first released in 2011 and described in a highly-cited publication in the Journal of Statistical Software, under the title [Glotaran: A Java-Based Graphical User Interface for the R Package TIMP](https://www.jstatsoft.org/article/view/v049i03) ([DOI: 10.18637/jss.v049.i03](https://dx.doi.org/10.18637/jss.v049.i03)).
 
 The [pyglotaran](https://github.com/glotaran/pyglotaran) software can be considered the spiritual successor of the [glotaran-legacy](https://github.com/glotaran/glotaran-legacy) software and has the backing of many of its original creators.
 

diff --git a/benchmark/asv.conf.json b/benchmark/asv.conf.json
@@ -51,7 +51,7 @@
   //"install_timeout": 600,
 
   // the base URL to show a commit for the project.
-  "show_commit_url": "http://github.com/glotaran/pyglotaran/commit/",
+  "show_commit_url": "https://github.com/glotaran/pyglotaran/commit/",
 
   // The Pythons you'd like to test against.  If not provided, defaults
   // to the current version of Python used to run `asv`.

diff --git a/changelog.md b/changelog.md
@@ -0,0 +1,93 @@
+# Changelog
+
+## 0.4.0 (2021-06-25)
+
+### ✨ Features
+
+- Add basic spectral model (#672)
+- Add Channel/Wavelength dependent shift parameter to irf. (#673)
+- Refactored Problem class into GroupedProblem and UngroupedProblem (#681)
+- Plugin system was rewritten (#600, #665)
+- Deprecation framework (#631)
+- Better notebook integration (#689)
+
+### 🩹 Bug fixes
+
+- Fix excessive memory usage in `_create_svd` (#576)
+- Fix several issues with KineticImage model (#612)
+- Fix exception in sdt reader index calculation (#647)
+- Avoid crash in result markdown printing when optimization fails (#630)
+- ParameterNotFoundException doesn't prepend '.' if path is empty (#688)
+- Ensure Parameter.label is str or None (#678)
+- Properly scale StdError of estimated parameters with RMSE (#704)
+- More robust covariance_matrix calculation (#706)
+- `ParameterGroup.markdown()` independent parametergroups of order (#592)
+
+### 🔌 Plugins
+
+- `ProjectIo` 'folder'/'legacy' plugin to save results (#620)
+- `Model` 'spectral-model' (#672)
+
+### 📚 Documentation
+
+- User documentation is written in notebooks (#568)
+- Documentation on how to write a `DataIo` plugin (#600)
+
+### 🗑️ Deprecations (due in 0.6.0)
+
+- `glotaran.ParameterGroup` -> `glotaran.parameterParameterGroup`
+- `glotaran.read_model_from_yaml` -> `glotaran.io.load_model(..., format_name="yaml_str")`
+- `glotaran.read_model_from_yaml_file` -> `glotaran.io.load_model(..., format_name="yaml")`
+- `glotaran.read_parameters_from_csv_file` -> `glotaran.io.load_parameters(..., format_name="csv")`
+- `glotaran.read_parameters_from_yaml` -> `glotaran.io.load_parameters(..., format_name="yaml_str")`
+- `glotaran.read_parameters_from_yaml_file` -> `glotaran.io.load_parameters(..., format_name="yaml")`
+- `glotaran.io.read_data_file` -> `glotaran.io.load_dataset`
+- `result.save` -> `glotaran.io.save_result(result, ..., format_name="legacy")`
+- `result.get_dataset("<dataset_name>")` -> `result.data["<dataset_name>"]`
+- `glotaran.analysis.result` -> `glotaran.project.result`
+- `glotaran.analysis.scheme` -> `glotaran.project.scheme`
+- `model.simulate` -> `glotaran.analysis.simulation.simulate(model, ...)`
+
+## 0.3.3 (2021-03-18)
+
+- Force recalculation of SVD attributes in `scheme._prepare_data` (#597)
+- Remove unneeded check in `spectral_penalties._get_area` Fixes (#598)
+- Added python 3.9 support (#450)
+
+## 0.3.2 (2021-02-28)
+
+- Re-release of version 0.3.1 due to packaging issue
+
+## 0.3.1 (2021-02-28)
+
+- Added compatibility for numpy 1.20 and raised minimum required numpy version to 1.20 (#555)
+- Fixed excessive memory consumption in result creation due to full SVD computation (#574)
+- Added feature parameter history (#557)
+- Moved setup logic to `setup.cfg` (#560)
+
+## 0.3.0 (2021-02-11)
+
+- Significant code refactor with small API changes to parameter relation specification (see docs)
+- Replaced lmfit with scipy.optimize
+
+## 0.2.0 (2020-12-02)
+
+- Large refactor with significant improvements but also small API changes (see docs)
+- Removed doas plugin
+
+## 0.1.0 (2020-07-14)
+
+- Package was renamed to `pyglotaran` on PyPi
+
+## 0.0.8 (2018-08-07)
+
+- Changed `nan_policiy` to `omit`
+
+## 0.0.7 (2018-08-07)
+
+- Added support for multiple shapes per compartment.
+
+## 0.0.6 (2018-08-07)
+
+- First release on PyPI, support for Windows installs added.
+- Pre-Alpha Development
diff --git a/docs/Doxyfile.ini b/docs/Doxyfile.ini
@@ -1130,7 +1130,7 @@ USE_HTAGS              = NO
 VERBATIM_HEADERS       = YES
 
 # If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
-# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
+# clang parser (see: https://clang.llvm.org/) for more accurate parsing at the
 # cost of reduced performance. This can be particularly helpful with template
 # rich C++ code for which doxygen's built-in parser lacks the necessary type
 # information.
@@ -1151,7 +1151,7 @@ VERBATIM_HEADERS       = YES
 # If clang assisted parsing is enabled you can provide the clang parser with the
 # path to the directory containing a file called compile_commands.json. This
 # file is the compilation database (see:
-# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) containing the
+# https://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) containing the
 # options used when the source files were built. This is equivalent to
 # specifying the "-p" option to a clang tool, such as clang-check. These options
 # will then be passed to the parser. Any options specified with CLANG_OPTIONS
@@ -1637,7 +1637,7 @@ USE_MATHJAX            = NO
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. See the MathJax site (see:
-# http://docs.mathjax.org/en/latest/output.html) for more details.
+# https://www.mathjax.org/) for more details.
 # Possible values are: HTML-CSS (which is slower, but has the best
 # compatibility), NativeMML (i.e. MathML) and SVG.
 # The default value is: HTML-CSS.
@@ -1667,7 +1667,7 @@ MATHJAX_EXTENSIONS     =
 
 # The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
 # of code that will be used on startup of the MathJax code. See the MathJax site
-# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
+# (see: https://www.mathjax.org/) for more details. For an
 # example see the documentation.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
@@ -2128,7 +2128,7 @@ DOCBOOK_PROGRAMLISTING = NO
 #---------------------------------------------------------------------------
 
 # If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
-# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures
+# AutoGen Definitions (see https://www.gnu.org/software/autogen/) file that captures
 # the structure of the code including all documentation. Note that this feature
 # is still experimental and incomplete at the moment.
 # The default value is: NO.
@@ -2329,7 +2329,7 @@ HIDE_UNDOC_RELATIONS   = NO
 
 # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
 # available from the path. This tool is part of Graphviz (see:
-# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
+# https://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
 # Bell Labs. The other options in this section have no effect if this option is
 # set to NO
 # The default value is: NO.
@@ -2484,7 +2484,7 @@ DIRECTORY_GRAPH        = YES
 # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
 # generated by dot. For an explanation of the image formats see the section
 # output formats in the documentation of the dot tool (Graphviz (see:
-# http://www.graphviz.org/)).
+# https://www.graphviz.org/)).
 # Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order
 # to make the SVG files visible in IE 9+ (other browsers do not have this
 # requirement).

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -2,6 +2,7 @@
 Sphinx>=3.2.0
 sphinx-rtd-theme>=0.5.1
 sphinx-copybutton>=0.3.0
+myst-parser>=0.12.0
 numpydoc>=0.8.0
 # notebook docs
 nbsphinx>=0.8.1

diff --git a/docs/source/changelog.md b/docs/source/changelog.md
@@ -0,0 +1,3 @@
+```{include} ../../changelog.md
+
+```
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -51,6 +51,7 @@
     "sphinx.ext.napoleon",
     "nbsphinx",
     "sphinx_last_updated_by_git",
+    "myst_parser",
     "numpydoc",
     "sphinx_copybutton",
 ]
@@ -70,8 +71,8 @@
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
-# source_suffix = ['.rst', '.md']
-source_suffix = ".rst"
+source_suffix = [".rst", ".md"]
+# source_suffix = ".rst"
 
 linkcheck_ignore = [
     r"https://github\.com/.+?#.+",

diff --git a/docs/source/history.rst b/docs/source/history.rst
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -13,7 +13,7 @@ Welcome to pyglotaran's documentation!
    introduction
    installation
    notebooks/quickstart/quickstart
-   history
+   changelog
    authors
 
 .. toctree::

diff --git a/docs/source/notebooks/quickstart/quickstart.ipynb b/docs/source/notebooks/quickstart/quickstart.ipynb
@@ -64,7 +64,7 @@
    "metadata": {},
    "source": [
     "Like all data in `pyglotaran`, the dataset is a [xarray.Dataset](https://xarray.pydata.org/en/stable/api.html#dataset).\n",
-    "You can find more information about the ``xarray`` library the [xarray hompage](http://xarray.pydata.org/en/stable/).\n",
+    "You can find more information about the ``xarray`` library the [xarray hompage](https://xarray.pydata.org/en/stable/).\n",
     "\n",
     "The loaded dataset is a simulated sequential model."
    ]

diff --git a/glotaran/__init__.py b/glotaran/__init__.py
@@ -8,7 +8,7 @@
 
 load_plugins()
 
-__version__ = "0.4.0.dev0"
+__version__ = "0.4.0"
 
 
 def __getattr__(attribute_name: str):

diff --git a/glotaran/analysis/optimize.py b/glotaran/analysis/optimize.py
@@ -108,11 +108,7 @@ def _create_result(
     parameters = problem.parameters
     covariance_matrix = None
     if success:
-        # robust covariance matrix calculation
-        # Refs:
-        # https://stackoverflow.com/a/67023688/3990615
-        # http://www.ceres-solver.org/nnls_covariance.html#_CPPv4N5ceres10Covariance7Options14algorithm_typeE
-        # https://www.cse.unr.edu/~bebis/CS791E/Notes/SVD.pdf
+        # See PR #706: More robust covariance matrix calculation
         _, jacobian_SV, jacobian_RSV = np.linalg.svd(jacobian, full_matrices=False)
         jacobian_SV_square = jacobian_SV ** 2
         mask = jacobian_SV_square > np.finfo(float).eps

diff --git a/setup.cfg b/setup.cfg
@@ -10,7 +10,8 @@ author_email = joern.weissenborn@gmail.com, j.snellenburg@gmail.com, i.h.m.van.s
 license = LGPL-3.0
 license_file = LICENSE
 classifiers =
-    Development Status :: 3 - Alpha
+    Development Status :: 4 - Beta
+    Intended Audience :: Education
     Intended Audience :: Science/Research
     License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
     Natural Language :: English
@@ -22,8 +23,9 @@ classifiers =
     Topic :: Scientific/Engineering :: Chemistry
     Topic :: Scientific/Engineering :: Physics
 project_urls =
-    GloTarAn Ecosystem=http://glotaran.org
-    Documentation=https://glotaran.readthedocs.io
+    Glotaran Ecosystem=https://glotaran.org
+    Documentation=https://pyglotaran.readthedocs.io
+    Changelog=https://pyglotaran.readthedocs.io/en/latest/changelog.html
     Source=https://github.com/glotaran/pyglotaran
     Tracker=https://github.com/glotaran/pyglotaran/issues