Include doc

build-deb.sh

@@ -3,7 +3,7 @@
 #    Project: FreeSaS
 #             https://github.com/kif/freesas
 #
-#    Copyright (C) 2015-2020 European Synchrotron Radiation Facility, Grenoble, France
+#    Copyright (C) 2015-2023 European Synchrotron Radiation Facility, Grenoble, France
 #
 #    Principal author:       Jérôme Kieffer ([email protected])
 #
@@ -56,12 +56,15 @@ then
             stretch)
                 debian_version=9
                 ;;
-            buster)  
+            buster)
                 debian_version=10
                 ;;
             bullseye)
                 debian_version=11
                 ;;
+            bookworm)
+                debian_version=12
+                ;;
         esac
     fi
 
@@ -78,21 +81,25 @@ build_directory=${project_directory}/build/${target_system}
 if [ -d /usr/lib/ccache ];
 then
    export PATH=/usr/lib/ccache:$PATH
+   export CCACHE_DIR=${HOME}/.ccache
 fi
 
 usage="usage: $(basename "$0") [options]
+
 Build the Debian ${debian_version} package of the ${project} library.
+
 If the build succeed the directory dist/debian${debian_version} will
 contains the packages.
+
 optional arguments:
     --help          Show this help text
     --install       Install the packages generated at the end of
                     the process using 'sudo dpkg'
     --stdeb-py3     Build using stdeb for python3
-    --stdeb-py2.py3 Build using stdeb for python2 and python3
     --debian9       Simulate a debian 9 Stretch system
     --debian10      Simulate a debian 10 Buster system
     --debian11      Simulate a debian 11 Bullseye system
+    --debian12      Simulate a debian 12 Bookworm system
 "
 
 install=0
@@ -141,6 +148,13 @@ do
           build_directory=${project_directory}/build/${target_system}
           shift
           ;;
+      --debian12)
+          debian_version=12
+          target_system=debian${debian_version}
+          dist_directory=${project_directory}/dist/${target_system}
+          build_directory=${project_directory}/build/${target_system}
+          shift
+          ;;
       -*)
           echo "Error: Unknown option: $1" >&2
           echo "$usage"
@@ -164,20 +178,27 @@ clean_up()
 build_deb() {
     tarname=${project}_${debianversion}.orig.tar.gz
     clean_up
-    python3 setup.py debian_src
-    python3 setup.py testdata
+    if [ $debian_version -le 11 ]
+    then
+       python3 setup.py debian_src
+       directory=${project}-${strictversion}
+    else
+       python3 -m build -s
+       ln -s ${source_project}-${strictversion}.tar.gz dist/${tarname}
+       directory=${source_project}-${strictversion}
+    fi
     cp -f dist/${tarname} ${build_directory}
     if [ -f dist/${project}-testimages.tar.gz ]
     then
       cp -f dist/${project}-testimages.tar.gz ${build_directory}
     fi
-    
+
     cd ${build_directory}
     tar -xzf ${tarname}
-    
-    directory=${project}-${strictversion}
+
+
     newname=${deb_name}_${debianversion}.orig.tar.gz
-    
+
     #echo tarname $tarname newname $newname
     if [ $tarname != $newname ]
     then
@@ -187,19 +208,19 @@ build_deb() {
       fi
         ln -s ${tarname} ${newname}
     fi
-    
+
     if [ -f ${project}-testimages.tar.gz ]
     then
       if [ ! -h  ${deb_name}_${debianversion}.orig-testimages.tar.gz ]
       then
         ln -s ${project}-testimages.tar.gz ${deb_name}_${debianversion}.orig-testimages.tar.gz
       fi
     fi
-    
+
     cd ${directory}
     cp -r ${project_directory}/package/${target_system} debian
     cp ${project_directory}/copyright debian
-    
+
     #handle test images
     if [ -f ../${deb_name}_${debianversion}.orig-testimages.tar.gz ]
     then
@@ -208,7 +229,7 @@ build_deb() {
         mkdir testimages
       fi
       cd testimages
-      tar -xzf  ../../${deb_name}_${debianversion}.orig-testimages.tar.gz
+      tar -xzf  ../${deb_name}_${debianversion}.orig-testimages.tar.gz
       cd ..
     else
       # Disable to skip tests during build
@@ -230,12 +251,12 @@ build_deb() {
             ;;
     esac
 
-    dch --force-distribution  -v ${debianversion}-1 "upstream development build of ${project} ${version}"
+    dch --force-distribution -v ${debianversion}-1 "upstream development build of ${project} ${version}"
     dch --force-distribution -D ${debian_name}-backports -l~bpo${debian_version}+ "${project} snapshot ${version} built for ${target_system}"
     #dch --bpo "${project} snapshot ${version} built for ${target_system}"
     dpkg-buildpackage -r
     rc=$?
-    
+
     if [ $rc -eq 0 ]; then
       # move packages to dist directory
       echo Build succeeded...
@@ -264,7 +285,8 @@ build_stdeb () {
     tar -xzf ${tarname}
     cd ${project}-${strictversion}
 
-    if [ $stdeb_all_python -eq 1 ]; then
+    if [ $stdeb_all_python -eq 1  ]
+    then
       echo Using Python 2+3
       python3 setup.py --command-packages=stdeb.command sdist_dsc --with-python2=True --with-python3=True --no-python3-scripts=True build --no-cython bdist_deb
       rc=$?
@@ -293,7 +315,7 @@ fi
 
 
 if [ $install -eq 1 ]; then
-  sudo -- su -c  "dpkg -i ${dist_directory}/*.deb"
+  sudo su -c  "dpkg -i ${dist_directory}/*.deb"
 fi
 
 exit "$rc"

build-doc.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python3
+import os
+import sys
+import logging
+import bootstrap
+from sphinx.cmd.build import main
+logger = logging.getLogger(__name__)
+PROJECT_DIR = os.path.dirname(os.path.abspath(__file__))
+PROJECT_NAME = bootstrap.get_project_name(PROJECT_DIR)
+logger.info("Project name: %s", PROJECT_NAME)
+LIBPATH = bootstrap.build_project(PROJECT_NAME, PROJECT_DIR)
+if __name__ == '__main__':
+    sys.path.insert(0, LIBPATH)
+    os.environ["PYTHONPATH"]=os.pathsep.join(sys.path)
+    print(os.environ["PYTHONPATH"])
+    dest_dir = os.path.join(PROJECT_DIR, "build", "sphinx")
+    if not os.path.isdir(dest_dir):
+        os.makedirs(dest_dir)
+    argv = ["-b", "html",
+            os.path.join(PROJECT_DIR,"doc","source"),
+            dest_dir ]
+    print(f"run sphinx with those arguments {argv}")
+    sys.exit(main(argv)) 

doc/source/conf.py

@@ -102,6 +102,7 @@
     'sphinx.ext.viewcode',
     'sphinx.ext.doctest',
     # 'sphinxext-archive',
+    'sphinxcontrib.programoutput',
     'nbsphinx'
 
 ]

e2etest/e2etest_bift.py

@@ -2,7 +2,7 @@
 
 __authors__ = ["Martha Brennich"]
 __license__ = "MIT"
-__date__ = "16/07/2021"
+__date__ = "29/11/2023"
 
 import unittest
 import pathlib
@@ -14,7 +14,7 @@
 import codecs
 import parse
 from numpy import loadtxt
-from freesas.test.utilstests import get_datafile
+from freesas.test.utilstest import get_datafile
 
 logger = logging.getLogger(__name__)
 

e2etest/e2etest_cormap.py

@@ -2,7 +2,7 @@
 
 __authors__ = ["Martha Brennich"]
 __license__ = "MIT"
-__date__ = "02/04/2022"
+__date__ = "29/11/2023"
 
 import unittest
 import pathlib
@@ -11,7 +11,7 @@
 from subprocess import run, PIPE, STDOUT
 from os import linesep
 from os.path import normpath
-from freesas.test.utilstests import get_datafile
+from freesas.test.utilstest import get_datafile
 
 logger = logging.getLogger(__name__)
 

e2etest/e2etest_freesas.py

@@ -25,7 +25,7 @@
 
 __authors__ = ["Martha Brennich"]
 __license__ = "MIT"
-__date__ = "16/07/2021"
+__date__ = "29/11/2023"
 
 import unittest
 import pathlib
@@ -34,7 +34,7 @@
 from subprocess import run, Popen, PIPE, STDOUT
 from os import linesep
 import PyPDF2
-from freesas.test.utilstests import get_datafile
+from freesas.test.utilstest import get_datafile
 
 logger = logging.getLogger(__name__)
 

e2etest/e2etest_guinier_apps.py

@@ -2,7 +2,7 @@
 
 __authors__ = ["Martha Brennich"]
 __license__ = "MIT"
-__date__ = "16/07/2021"
+__date__ = "29/11/2023"
 
 import unittest
 import pathlib
@@ -11,7 +11,7 @@
 from os import linesep
 from os.path import normpath
 from platform import system
-from freesas.test.utilstests import get_datafile
+from freesas.test.utilstest import get_datafile
 logger = logging.getLogger(__name__)
 
 

package/debian12/changelog

@@ -0,0 +1,5 @@
+freesas (0.7.0-1) unstable; urgency=low
+
+  * Initial release (Closes: #??????)
+
+ -- Jerome Kieffer <[email protected]>  Fri, 31 Aug 2017 11:00:20 +0100

package/debian12/clean

@@ -0,0 +1 @@
+*.egg-info/*

package/debian12/compat

@@ -0,0 +1 @@
+10

package/debian12/control

@@ -0,0 +1,66 @@
+Source: freesas
+Maintainer: Debian Science Maintainers <[email protected]>
+Uploaders: Jerome Kieffer <[email protected]>,
+           Picca Frédéric-Emmanuel <[email protected]>
+Section: science
+Priority: extra
+Build-Depends: cython3,
+               debhelper (>=9.20150101+deb8u2),
+               python3-all-dev,
+               python3-setuptools,
+               python3-numpy,
+               python3-matplotlib,
+               python3-scipy,
+               python3-sphinx,
+               python3-sphinxcontrib.programoutput,
+               python3-nbsphinx,
+               python3-silx,
+               python3-pyfai,
+               openstack-pkg-tools,
+               help2man,
+               dh-python,
+               python3-sphinx-rtd-theme
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-science/packages/freesas.git
+Vcs-Git: git://anonscm.debian.org/debian-science/packages/freesas.git
+Homepage: https://github.com/kif/freesas
+X-Python3-Version: >= 3.6
+
+Package: freesas
+Architecture: all
+Depends: ${misc:Depends},
+         ${python:Depends},
+         ${shlibs:Depends},
+         python3-pkg-resources,
+         python3-freesas (>= ${source:Version})
+Description: Free tools for small angle scattering analysis - Executables
+ .
+ This uses the Python 3 version of the package.
+
+
+Package: python3-freesas
+Architecture: any
+Section: python
+Depends: ${misc:Depends},
+         ${python3:Depends},
+         ${shlibs:Depends},
+         python3-numpy,
+         python3-matplotlib,
+         python3-scipy,
+         python3-six,
+         python3-pyfai
+# Recommends:
+# Suggests: python3-rfoo
+Description: Free tools for small angle scattering analysis - Python3
+ .
+ This is the Python 3 version of the package.
+
+
+Package: python-freesas-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends},
+         ${sphinxdoc:Depends}
+Description: Free tools for small angle scattering analysis - Documentation
+ .
+ This is the common documentation package.

package/debian12/gbp.conf

@@ -0,0 +1,2 @@
+[DEFAULT]
+debian-branch = master

package/debian12/python-freesas-doc.doc-base

@@ -0,0 +1,9 @@
+Document: freesas-manual
+Title: freesas documentation manual
+Author: Jérôme Kieffer <[email protected]>
+Abstract: Toolbox for X-Ray data analysis 
+Section: Science/Data Analysis
+
+Format: HTML
+Index: /usr/share/doc/python-freesas-doc/html/index.html
+Files: /usr/share/doc/python-freesas-doc/html/*