75 organizing python modules (#76)

* First reorganization and cleaning.
* New directory structure.
* Refactoring scripts to satisfy linters.
* Organizing notebooks.
* Reorganizing notebooks, new MCMC tests with gaussian mixture models.
* Organizing python scripts and support in NumCosmoPy.
* Refactored mcat_calibrate_apes.py.
* New interpolation object.
* Improving getdist (added asinh filter).
* Added check for unclean notebooks.
* Cleaning notebooks.
* Checking notebooks first in GHA.
* Normalizing filenames and organizing Makefile.am.
* Using lower-case names for notebooks.
* Updated Makefile.am.

.github/workflows/build_check.yml

@@ -18,6 +18,8 @@ jobs:
     - uses: actions/checkout@v2
     - name: Install prereq
       run: sudo apt-get install gobject-introspection gir1.2-glib-2.0 libgirepository1.0-dev gcc gfortran pkg-config libglib2.0-dev libgmp3-dev libmpfr-dev libgsl0-dev libfftw3-dev libopenblas-dev libflint-arb-dev libcfitsio-dev libnlopt-dev libhdf5-dev gtk-doc-tools texlive texlive-bibtex-extra texlive-science texlive-publishers tex4ht perl libxml-libxml-perl
+    - name: Ensure clear Jupyter Notebooks
+      uses: ResearchSoftwareActions/EnsureCleanNotebooksAction@1.1
     - name: Autogen
       run: NOCONFIGURE=yes ./autogen.sh
     - name: configure
@@ -86,6 +88,8 @@ jobs:
         brew install autoconf automake libtool gobject-introspection gsl gmp mpfr fftw cfitsio nlopt gfortran gtk-doc glib-utils glib
         brew ls glib
         brew ls glib-utils
+    - name: Ensure clear Jupyter Notebooks
+      uses: ResearchSoftwareActions/EnsureCleanNotebooksAction@1.1
     - name: Autogen
       run: NOCONFIGURE=yes ./autogen.sh
     - name: configure

configure.ac

@@ -1092,7 +1092,6 @@ examples/Makefile
 examples/model_mcmc/Makefile
 examples/pydata_simple/Makefile
 notebooks/Makefile
-notebooks/tutorials/Makefile
 data/Makefile
 numcosmo/build_cfg.h
 ])

docs/numcosmo-docs.sgml

@@ -185,6 +185,7 @@
       <xi:include href="xml/ncm_data_gauss_cov_mvnd.xml"/>
       <xi:include href="xml/ncm_model_rosenbrock.xml"/>
       <xi:include href="xml/ncm_data_rosenbrock.xml"/>
+      <xi:include href="xml/ncm_data_gaussmix2d.xml"/>
       <xi:include href="xml/ncm_model_funnel.xml"/>
       <xi:include href="xml/ncm_data_funnel.xml"/>
     </section>   

examples/example_apes.py

@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+#
+# example_apes.py
+#
+# Wed Feb 8 10:00:00 2023
+# Copyright  2023  Sandro Dias Pinto Vitenti
+# <vitenti@uel.br>
+#
+# example_apes.py
+# Copyright (C) 2023 Sandro Dias Pinto Vitenti <vitenti@uel.br>
+#
+# numcosmo is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# numcosmo 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""Example of using the APES MCMC sampler on test posteriors."""
+
+import typer
+from numcosmo_py import Ncm
+from numcosmo_py.experiments.rosenbrock import run_rosenbrock_mcmc
+from numcosmo_py.experiments.gaussmix2d import run_gaussmix2d_mcmc
+from numcosmo_py.experiments.funnel import run_funnel_mcmc
+
+
+Ncm.cfg_init()
+app = typer.Typer()
+
+app.command()(run_rosenbrock_mcmc)
+app.command()(run_gaussmix2d_mcmc)
+app.command()(run_funnel_mcmc)
+
+if __name__ == "__main__":
+    app()