Merge pull request #6 from clinssen/v2.3.1-docs

Cleanup and Docker image (release version 2.3.2)

.github/workflows/pygsl-ci.yml

@@ -29,13 +29,13 @@ jobs:
       - name: Python dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install pytest numpy scipy matplotlib
+          python -m pip install pytest numpy scipy matplotlib wheel setuptools
           python -m pip install pycodestyle
 
       # Static code analysis
       #- name: Static code style analysis
       #  run: |
-      #    python3 extras/codeanalysis/check_copyright_headers.py && python3 -m pycodestyle $GITHUB_WORKSPACE -v --ignore=E241,E501,E303,E714,E713,E714,E252,W503 --exclude=$GITHUB_WORKSPACE/doc,$GITHUB_WORKSPACE/.github
+      #    python3 -m pycodestyle $GITHUB_WORKSPACE -v --ignore=E241,E501,E303,E714,E713,E714,E252,W503 --exclude=$GITHUB_WORKSPACE/doc,$GITHUB_WORKSPACE/.github
 
       - name: config
         run: |

ChangeLog

@@ -1,4 +1,7 @@
-2016-04          Pierre Schnizer <schnizer@user.sourceforge.net>	
+v2.3.2 (2021-12) Charl Linssen <c.linssen@fz-juelich.de>
+	* Support for pip installing pygsl on Linux systems.
+
+2016-04          Pierre Schnizer <schnizer@user.sourceforge.net>
 	* Started refurbishment of gsl sf interface generators
 	* Added sf tests: translated from gsl source
 	* Added interpolation2d

MANIFEST.in

@@ -53,3 +53,4 @@ include MANIFEST.in
 include MANIFEST
 include COPYING
 
+include testing/src/sf/sf.i

README.rst

@@ -66,10 +66,11 @@ PyGSL is installed to the Python packages path, and can be uninstalled by typing
 Installation via PyPI
 ---------------------
 
-PyGSL can also be installed using the pip package installer. Simply type:
+PyGSL can also be installed using the pip package installer. This requires the Python packages ``setuptools`` and ``wheel`` to be already installed. Simply type:
 
 .. code-block:: sh
 
+   python -m pip install setuptools wheel
    python -m pip install pygsl
 
 To remove PyGSL, use:

doc/release_checklist.rst

@@ -0,0 +1,26 @@
+Checklist for releasing a new version on PyPI
+---------------------------------------------
+
+- Adapt the version numbers in ``pygsl/_version.py`` and ``setup.cfg``
+
+- Build the wheels
+
+  .. code-block:: sh
+
+     python setup.py sdist
+
+- Do a test upload
+
+  .. code-block:: sh
+
+     twine upload --repository testpypi dist/* 
+
+- Try to install it from a docker image
+
+  .. code-block:: sh
+
+     python3 -m pip install --index-url https://test.pypi.org/simple/ pygsl
+
+- Clone the repository and run the tests via pytest
+
+- Happy? Push to non-testing repository

docker/Dockerfile

@@ -0,0 +1,40 @@
+FROM ubuntu:focal
+LABEL maintainer="https://github.com/pygsl/pygsl"
+
+ENV TERM=xterm \
+    TZ=Europe/Berlin \
+    DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential libtool automake autotools-dev \
+    nano \
+    swig \
+    libgsl-dev \
+    python3-dev \
+    python3-ipython \
+    python3-matplotlib \
+    python3-numpy \
+    python3-pip \
+    python3-scipy \
+    python3-setuptools \
+    cmake wget git curl && \
+    rm -rf /var/lib/apt/lists/* && \
+    update-alternatives --install /usr/bin/python python /usr/bin/python3 10 && \
+    update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
+
+RUN python3 -m pip install --upgrade pip setuptools wheel pytest
+#RUN python3 -m pip install --index-url https://test.pypi.org/simple/ pygsl
+RUN python3 -m pip install pygsl
+
+# add user 'user'
+RUN adduser --disabled-login --gecos 'USER' --home /home/user user && \
+    chown user:user /home/user
+
+# copy entrypoint to user home folder
+COPY entrypoint.sh /home/user
+RUN chown user:user /home/user/entrypoint.sh && \
+    chmod +x /home/user/entrypoint.sh
+
+WORKDIR /home/user
+USER user
+ENTRYPOINT ["/home/user/entrypoint.sh"]

docker/entrypoint.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+/bin/bash
+

pygsl/_version.py

@@ -1 +1 @@
-version = "2.3.1"
+version = "2.3.2"

setup.cfg

@@ -7,15 +7,15 @@ doc_files = ChangeLog
 	TODO
 	doc/
 	examples/
-requires = python >= 2.2, python-numeric, gsl >= 1.2
+requires = python >= 3, python-numeric, gsl >= 1.2
 build_requires = python-numeric-devel, gsl-devel >= 1.2
 vendor = https://github.com/pygsl/pygsl
 description = This project provides a python interface for the GNU scientific library (gsl).
 
 [build_sphinx]
 project = 'pygsl'
-version = 2.3.1
-release = 2.3.1
+version = 2.3.2
+release = 2.3.2
 
 [egg_info]
 tag_build = 

setup.py

@@ -76,6 +76,7 @@
 # Add the gsldist path
 import os
 pygsldir = os.path.dirname("__name__")
+
 # Get the version information
 versionfile = open(os.path.join(pygsldir, "pygsl", "_version.py"))
 versiontext = versionfile.read()
@@ -88,21 +89,19 @@
 gsldist_path = os.path.join(pygsldir, "gsl_dist")
 sys.path.insert(0, gsldist_path)
 
+from wheel.bdist_wheel import bdist_wheel as _bdist_wheel
 
-#import distutils
-#from distutils.core import setup, Extension
+import setuptools
+import setuptools.command
+import setuptools.command.install
+import setuptools.command.bdist_egg
 from setuptools import setup, Extension
 
-# used to read array object ... do not need that any more
-# import gsl_numobj
-
 from gsl_Extension import gsl_Extension
 from swig_extension import SWIG_Extension as _SWIG_Extension
 from swig_extension import SWIG_Extension_Nop as _SWIG_Extension_Nop
 
 from distutils import sysconfig
-#from common_objects import libpygsl
-
 
 
 if USE_SWIG == 0:
@@ -160,7 +159,7 @@ def SWIG_Extension(*args, **kws):
     pass
 else:
     assert(_has_gsl_config)
-    #Just checking that the module is there    
+    #Just checking that the module is there
     gsl_features
 
     # now gsl_packages can be loaded. Using gsl_features only the available ones
@@ -172,9 +171,27 @@ def SWIG_Extension(*args, **kws):
     del text
     t_file.close()
     del t_file
-
 
 
+class CustomInstallCommand(setuptools.command.install.install):
+    def run(self):
+        # first re-generate GSL wrappers using SWIG
+        self.run_command('gsl_wrappers')
+        # then configure
+        self.run_command('config')
+        # then install
+        setuptools.command.install.install.run(self)
+        #super().run()
+
+class CustomBdistWheelCommand(_bdist_wheel):
+    def run(self):
+        # first re-generate GSL wrappers using SWIG
+        self.run_command('gsl_wrappers')
+        # then configure
+        self.run_command('config')
+        # then install
+        _bdist_wheel.run(self)
+        #super().run()
 
 py_module_names = ['errors',
                    'statistics.__init__',
@@ -222,19 +239,20 @@ def SWIG_Extension(*args, **kws):
     headers = glob.glob("Include/pygsl/*.h")
     gsldist = ['gsl_dist.' + os.path.basename(x)[:-3] for x in glob.glob("gsl_dist/*.py")]
 
-py_modules = ['pygsl.' + x for x in py_module_names] + gsldist 
+py_modules = ['pygsl.' + x for x in py_module_names] + gsldist
 
 if sys.version_info[0] <= 2:
     exts = exts + extsOnly2
     sys.stdout.write("Bulding for '%s'\n" %(sys.version,))
-    
+
 
 class gsl_Config_Path(gsl_Config.gsl_Config):
     """
     Only required here to set the pygsl directory
     """
     _pygsl_dir = pygsldir
 
+
 print("#%d extension modules" %(len(exts),))
 
 proj_name ="pygsl"
@@ -252,8 +270,10 @@ class gsl_Config_Path(gsl_Config.gsl_Config):
        ext_package = 'pygsl',
        ext_modules = exts,
        headers = headers,
-       cmdclass = {'config' : gsl_Config_Path,
+       cmdclass = {'bdist_wheel': CustomBdistWheelCommand,
+                   'config' : gsl_Config_Path,
                    'gsl_wrappers': gsl_CodeGenerator.gsl_CodeGenerator,
+                   'install': CustomInstallCommand,
                    #'build_sphinx': BuildDoc
                    },
        install_requires = ['numpy'],
@@ -262,5 +282,6 @@ class gsl_Config_Path(gsl_Config.gsl_Config):
                'project': ('setup.py', proj_name),
                'version': ('setup.py', version),
                }
-            }
+            },
+       package_data={"pygsl": ["testing/src/sf/sf.i"]}
        )

testing/src/sf/sf.i

@@ -0,0 +1,136 @@
+%module sf
+
+#include <pygsl/pygsl_features_config.h>
+%ignore gsl_sf_angle_restrict_pos_e; // use a double * for input and output. not properly recognized.
+// use gsl_sf_angle_restricted_pos_err_e complies to the usual interface
+%ignore gsl_sf_result_smash_e; // the only one to use a const pointer as input. Not recognized by the tool.
+
+
+%include <gsl/gsl_sf_result.h>
+
+//Deprecated functions
+%ignore gsl_sf_coupling_6j_INCORRECT_e;
+%ignore gsl_sf_coupling_6j_INCORRECT;
+
+// Not a direct map
+%ignore gsl_sf_polar_to_rect;
+%ignore gsl_sf_rect_to_polar;
+
+// Functions returning arrays are not mapped currently.
+
+%ignore gsl_sf_gegenpoly_array;
+
+
+%include <gsl/gsl_sf_airy.h>
+
+%ignore gsl_sf_bessel_sequence_Jnu_e;
+%ignore gsl_sf_bessel_Jn_array;
+%ignore gsl_sf_bessel_Yn_array;
+%ignore gsl_sf_bessel_In_array;
+%ignore gsl_sf_bessel_In_scaled_array;
+%ignore gsl_sf_bessel_Kn_array;
+%ignore gsl_sf_bessel_Kn_scaled_array;
+%ignore gsl_sf_bessel_jl_array;
+%ignore gsl_sf_bessel_jl_steed_array;
+%ignore gsl_sf_bessel_yl_array;
+%ignore gsl_sf_bessel_il_scaled_array;
+%ignore gsl_sf_bessel_kl_scaled_array;
+%include <gsl/gsl_sf_bessel.h>
+%include <gsl/gsl_sf_clausen.h>
+
+%ignore gsl_sf_coulomb_wave_F_array;           
+%ignore gsl_sf_coulomb_wave_FG_array;
+%ignore gsl_sf_coulomb_wave_FGp_array;
+%ignore gsl_sf_coulomb_wave_sphF_array;
+%ignore gsl_sf_coulomb_CL_array;
+%include <gsl/gsl_sf_coulomb.h>
+
+%include <gsl/gsl_sf_coupling.h>
+%include <gsl/gsl_sf_dawson.h>
+%include <gsl/gsl_sf_debye.h>
+%include <gsl/gsl_sf_dilog.h>
+%include <gsl/gsl_sf_elementary.h>
+%include <gsl/gsl_sf_ellint.h>
+%include <gsl/gsl_sf_elljac.h>
+%include <gsl/gsl_sf_erf.h>
+%include <gsl/gsl_sf_exp.h>
+%include <gsl/gsl_sf_expint.h>
+%include <gsl/gsl_sf_fermi_dirac.h>
+%include <gsl/gsl_sf_gamma.h>
+%include <gsl/gsl_sf_gegenbauer.h>
+%include <gsl/gsl_sf_hyperg.h>
+%include <gsl/gsl_sf_laguerre.h>
+%include <gsl/gsl_sf_lambert.h>
+
+
+%ignore gsl_sf_legendre_Pl_array;
+%ignore gsl_sf_legendre_Pl_deriv_array;
+%ignore gsl_sf_legendre_Plm_array;
+%ignore gsl_sf_legendre_Plm_deriv_array;
+%ignore gsl_sf_legendre_sphPlm_array;
+%ignore gsl_sf_legendre_sphPlm_deriv_array;
+%ignore gsl_sf_legendre_array_size;
+%ignore gsl_sf_legendre_H3d_array;
+%ignore gsl_sf_legendre_array;
+%ignore gsl_sf_legendre_array_e;
+%ignore gsl_sf_legendre_deriv_array_e;
+%ignore gsl_sf_legendre_deriv_array;
+%ignore gsl_sf_legendre_deriv_alt_array;
+%ignore gsl_sf_legendre_deriv_alt_array_e;
+%ignore gsl_sf_legendre_deriv2_array;
+%ignore gsl_sf_legendre_deriv2_array_e;
+%ignore gsl_sf_legendre_deriv2_alt_array;
+%ignore gsl_sf_legendre_deriv2_alt_array_e;
+%ignore gsl_sf_legendre_array_n;
+%ignore gsl_sf_legendre_array_index;
+%ignore gsl_sf_legendre_nlm;
+%include <gsl/gsl_sf_legendre.h>
+%include <gsl/gsl_sf_log.h>
+
+ /* */
+#ifdef _PYGSL_GSL_HAS_SF_MATHIEU
+%ignore gsl_sf_mathieu_ce_array;
+%ignore gsl_sf_mathieu_se_array;
+%ignore gsl_sf_mathieu_Mc_array;
+%ignore gsl_sf_mathieu_Ms_array;
+%ignore gsl_sf_mathieu_a_array;
+%ignore gsl_sf_mathieu_b_array;
+%ignore gsl_sf_mathieu_workspace;
+%ignore gsl_sf_mathieu_free;
+%ignore gsl_sf_mathieu_alloc;
+%ignore gsl_sf_mathieu_a_coeff;
+%ignore gsl_sf_mathieu_b_coeff;
+
+%include <gsl/gsl_sf_mathieu.h>
+#endif
+
+ /* */
+%include <gsl/gsl_sf_pow_int.h>
+%include <gsl/gsl_sf_psi.h>
+%include <gsl/gsl_sf_synchrotron.h>
+%include <gsl/gsl_sf_transport.h>
+%include <gsl/gsl_sf_trig.h>
+%include <gsl/gsl_sf_zeta.h>
+
+
+
+// Complex Functions are wrapped manually.
+//%ignore gsl_sf_complex_dilog_e;   // polar to rect
+//%ignore gsl_sf_lngamma_complex_e; // rect to polar
+//%ignore gsl_sf_complex_log_e;     // rect to polar
+//%ignore gsl_sf_complex_sin_e;     // rect to rect
+//%ignore gsl_sf_complex_cos_e;     // rect to rect
+//%ignore gsl_sf_complex_logsin_e;  
+
+
+
+#define INLINE_DECL
+%include <gsl/gsl_complex_math.h>
+ //%ignore gsl_complex_sqrt_real;
+ //%ignore gsl_complex_polar;
+ //%ignore gsl_complex_polar;
+
+%ignore gsl_coerce_float;
+%ignore gsl_coerce_long_double;
+%include <gsl/gsl_sys.h>
+%ignore gsl_coerce_float;