Update package versions

README.rst

@@ -1,18 +1,19 @@
 ShapePipe
 =========
 
-|CI| |CD| |python38|
+|CI| |CD| |python39| |release|
 
 .. |CI| image:: https://github.com/CosmoStat/shapepipe/workflows/CI/badge.svg
   :target: https://github.com/CosmoStat/shapepipe/actions?query=workflow%3ACI
 
 .. |CD| image:: https://github.com/CosmoStat/shapepipe/actions/workflows/pages/pages-build-deployment/badge.svg
   :target: https://github.com/CosmoStat/shapepipe/actions/workflows/pages/pages-build-deployment
 
-.. |python38| image:: https://img.shields.io/badge/python-3.8-green.svg
-  :target: https://www.python.org/
+.. |python39| image:: https://img.shields.io/badge/python-3.9-green.svg
+  :target: https://www.python.org/‰
 
-:Version: 0.0.4
+.. |release| image:: https://img.shields.io/github/v/release/CosmoStat/shapepipe
+  :target: https://github.com/CosmoStat/shapepipe/releases/latest
 
 ShapePipe is a galaxy shape measurement pipeline developed within the
 CosmoStat lab at CEA Paris-Saclay.

docs/requirements.txt

@@ -1,5 +1,5 @@
-myst-parser>=0.16.1
-numpydoc>=1.1.0
-sphinx>=4.3.1
-sphinxcontrib-bibtex>=2.4.1
-sphinx-book-theme>=0.1.10
+myst-parser==0.17.0
+numpydoc==1.2
+sphinx==4.4.0
+sphinxcontrib-bibtex==2.4.1
+sphinx-book-theme==0.2.0

docs/source/conf.py

@@ -23,9 +23,9 @@
 author = 'CosmoStat'
 
 # The short X.Y version
-version = '0.0'
+version = '1.0'
 # The full version, including alpha/beta/rc tags
-release = '0.0.4'
+release = '1.0.0'
 
 
 # -- General configuration ---------------------------------------------------

environment.yml

@@ -2,30 +2,30 @@ name: shapepipe
 channels:
   - conda-forge
 dependencies:
-  - python=3.8
-  - pip>=21
-  - astropy==4.1
+  - python=3.9
+  - pip>=21.2.4
+  - astropy==5.0
   - automake==1.16.2
   - autoconf==2.69
   - cmake==3.19.6
   - galsim==2.2.5
-  - joblib==1.0.1
+  - joblib==1.1.0
   - libtool==2.4.6
-  - matplotlib==3.3.4
+  - matplotlib==3.5.1
+  - numba==0.54.1
+  - pandas==1.4.1
   - pip:
-    - mccd==1.2.1
-    - modopt==1.5.1
-    - numba==0.53.1
-    - pandas==1.2.4
-    - PyQt5==5.15.4
-    - pyqtgraph==0.11.1
-    - python-pysap==0.0.5
-    - reproject==0.7.1
+    - mccd==1.2.3
+    - modopt==1.6.0
+    - PyQt5==5.15.6
+    - pyqtgraph==0.12.4
+    - python-pysap==0.0.6
+    - reproject==0.8
     - sip_tpv==1.1
     - sf_tools==2.0.4
-    - sqlitedict==1.7.0
+    - sqlitedict==2.0.0
     - termcolor==1.1.0
-    - tqdm==4.60.0
-    - treecorr==4.1.7
+    - tqdm==4.63.0
+    - treecorr==4.2.6
     - git+https://github.com/aguinot/ngmix@stable_version
     - git+https://github.com/tobias-liaudat/Stile@v0.1

install_shapepipe

@@ -10,14 +10,21 @@ export LC_CTYPE=en_US.utf8
 #
 ##############################################################################
 
-version="1.5"
+version="1.6"
+last_update="08/03/22"
 
 ##############################################################################
 # EXTERNAL PACKAGES AND SCRIPTS
 ##############################################################################
 
 # External packages
 
+# Conda package versions
+fftw_ver="3.3.10"
+libpng_ver="1.6.37"
+mpi4py_ver="3.1.3"
+openblas_ver="0.3.18"
+
 # SExtractor Package
 sex_url="https://github.com/astromatic/sextractor/archive/2.25.0.tar.gz"
 sex_tar="2.25.0.tar.gz"
@@ -47,9 +54,9 @@ cdsclient_bin="findgsc2.2"
 cdsclient_version=FALSE
 
 # mpi4py Package
-mpi_url="https://github.com/mpi4py/mpi4py/archive/3.0.3.tar.gz"
-mpi_tar="3.0.3.tar.gz"
-mpi_dir="mpi4py-3.0.3"
+mpi_url="https://github.com/mpi4py/mpi4py/archive/${mpi4py_ver}.tar.gz"
+mpi_tar="${mpi4py_ver}.tar.gz"
+mpi_dir="mpi4py-${mpi4py_ver}"
 mpi_bin="mpiexec"
 mpi_version=TRUE
 
@@ -251,7 +258,7 @@ check_binary2() {
 
 # Check if a python site-package is installed correctly in the conda environment
 check_site_pkg() {
-  if compgen -G "$CONDA_PREFIX/lib/python3.8/site-packages/$1*" > /dev/null
+  if compgen -G "$CONDA_PREFIX/lib/python3.*/site-packages/$1*" > /dev/null
   then
     echo -ne "   - $1:\t \xe2\x9c\x85\n"
   else
@@ -276,7 +283,7 @@ start() {
   echo ''
   echo 'Author: Samuel Farrens'
   echo 'Version:' $version
-  echo 'Last Update: 26/01/2022'
+  echo 'Last Update:' $last_update
   echo $line
   echo ''
 }
@@ -698,7 +705,7 @@ then
   report_progress 'MPI'
   if [ -z "$MPI_ROOT" ]
   then
-    conda install -n $ENV_NAME -c conda-forge "mpi4py>=3.0.1" -y
+    conda install -n $ENV_NAME -c conda-forge "mpi4py==${mpi4py_ver}" -y
   else
     download_package $mpi_url $mpi_tar
     build_mpi $mpi_dir
@@ -713,13 +720,13 @@ fi
 if [ "$INSTALL_SEX" == TRUE ] && check_binary $sex_bin
 then
   report_progress 'SExtractor'
-  conda install -n $ENV_NAME -c conda-forge fftw -y
+  conda install -n $ENV_NAME -c conda-forge "fftw==${fftw_ver}" -y
   download_package $sex_url $sex_tar
   if [ "$use_atlas" == TRUE ]
   then
     build_sex_atlas $sex_dir
   else
-    conda install -n $ENV_NAME -c conda-forge openblas -y
+    conda install -n $ENV_NAME -c conda-forge "openblas==${openblas_ver}" -y
     build_sex_blas $sex_dir
   fi
 fi
@@ -728,14 +735,14 @@ fi
 if [ "$INSTALL_PSFEX" == TRUE ] && check_binary $psfex_bin
 then
   report_progress 'PSFEx'
-  conda install libpng -y
-  conda install -n $ENV_NAME -c conda-forge fftw -y
+  conda install "libpng==${libpng_ver}" -y
+  conda install -n $ENV_NAME -c conda-forge "fftw==${fftw_ver}" -y
   download_package $psfex_url $psfex_tar
   if [ "$use_atlas" == TRUE ]
   then
     build_psfex_atlas $psfex_dir
   else
-    conda install -n $ENV_NAME -c conda-forge openblas -y
+    conda install -n $ENV_NAME -c conda-forge "openblas==${openblas_ver}" -y
     build_psfex_blas $psfex_dir
   fi
 fi

shapepipe/info.py

@@ -15,7 +15,7 @@
 
 
 # Package Info
-version_info = (0, 0, 4)
+version_info = (1, 0, 0)
 __version__ = '.'.join(str(c) for c in version_info)
 __name__ = 'shapepipe'
 __author__ = 'Samuel Farrens'

shapepipe/utilities/galaxy.py

@@ -47,14 +47,14 @@ def sigma_to_fwhm(sigma, pixel_scale=1.0):
     -----
     To compute the FWHMh for a 1D Gaussian N(x), solve the equation
 
-    ..math::
+    .. math::
 
         N(x) = (\sigma \sqrt{2\pi})^{-1} \exp[x^2/2\sigma^2] = \frac 1 2 N(x)
 
 
     for :math:`x`. The FWHM is :math:`x + (-x) = 2x`. The solution is
 
-    ..math::
+    .. math::
 
         \textrm{FWHM} = 2 \sqrt(2 \ln 2) \sigma \approx 2.355 \sigma