Trac #21441: Old installed version of Cython is used

On a machine which had an older version of Cython installed but which was upgraded recently after #20218 was merged: {{{ $ ls -ld local/lib/python/site-packages/Cython* drwxrwxr-x 12 jdemeyer jdemeyer 4096 Sep 6 21:23 local/lib/python/site- packages/Cython drwxrwxr-x 5 jdemeyer jdemeyer 4096 Sep 6 21:22 local/lib/python/site- packages/Cython-0.23.3-py2.7-linux-i686.egg drwxrwxr-x 2 jdemeyer jdemeyer 4096 Sep 6 21:14 local/lib/python/site- packages/Cython-0.24.1-py2.7.egg-info }}} Despite Cython-0.24.1 being available, the older version 0.23.3 is still used by default. This causes breakage when building the Sage library. {{{ >>> import Cython >>> Cython.__version__ '0.23.3' >>> import sys >>> [x for x in sys.path if 'Cython' in x] ['/home/jdemeyer/sage-git/local/lib/python2.7/site- packages/Cython-0.23.3-py2.7-linux-i686.egg'] }}} The problem is not limited to Cython, the same happens for other packages too. This is a blocker ticket since it breaks upgrades from older Sage versions. '''Steps to reproduce''': 1. `./sage --sh -c 'easy_install cython==0.23.3'` # Install an older version of Cython. 2. `./sage -f cython` # Rebuild the Cython in Sage. This ''should'' uninstall the old version but it doesn't. '''Note to the release manager''': ideally, this would be merged together with #21552 since both tickets trigger recompilation of all Python packages. URL: https://trac.sagemath.org/21441 Reported by: jdemeyer Ticket author(s): Erik Bray, Jeroen Demeyer Reviewer(s): Jeroen Demeyer, Erik Bray, Matthias Koeppe
sagemath · Oct 3, 2016 · 2f8fc1e · 2f8fc1e
2 parents 3678936 + 8fd8273
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diff --git a/build/bin/sage-pip-install b/build/bin/sage-pip-install
@@ -0,0 +1,67 @@
+#!/usr/bin/env bash
+# This command is specifically for pip-installing from a local
+# source directory, as opposed to from a package index via package
+# name.  That is, it is for pip-installing Sage spkgs from their
+# extracted upstream sources.
+#
+# This ensures that any previous installations of the same package
+# are uninstalled first.
+
+# Default arguments for all packages installed with `pip install`
+# --ignore-installed : Force pip to re-install package even if it thinks it's
+#                      already installed (for which it sometimes gets false
+#                      positives for partially-installed packages).
+# --verbose          : Display the output when running setup.py.
+# --no-deps          : Don't install runtime dependencies from PyPI.
+# --no-index         : Don't look at the package index.
+#                      This also disables pip's version self-check.
+pip_install_flags="--ignore-installed --verbose --no-deps --no-index"
+
+# Consume any additional pip install arguments except the last one
+while [ $# -gt 1 ]; do
+    pip_install_flags="$pip_install_flags $1"
+    shift
+done
+
+# Last argument must be "." and will be ignored
+if [ "$1" != "." ]; then
+    echo >&2 "$0 requires . as final argument"
+    exit 1
+fi
+
+# Find out the name of the package that we are installing
+name="$(python setup.py --name)"
+
+if [ $? -ne 0 ]; then
+    echo >&2 "Error: could not determine package name"
+    exit 1
+fi
+
+if [ $(echo "$name" | wc -l) -gt 1 ]; then
+    name="$(echo "$name" | tail -1)"
+    echo >&2 "Warning: This package has a badly-behaved setup.py which outputs"
+    echo >&2 "more than the package name for 'setup.py --name'; using the last"
+    echo >&2 "line as the package name: $name"
+fi
+
+# Keep uninstalling as long as it succeeds
+while true; do
+    out=$(pip uninstall --disable-pip-version-check -y "$name" 2>&1)
+    if [ $? -ne 0 ]; then
+        break
+    fi
+    echo "$out"
+done
+
+# Not ideal, but this is the easiest way to check if the package
+# was not installed to begin with (which pip treats as an error).
+# If it wasn't, then we proceed quietly; if it was installed show the
+# uninstallation output and error out.
+if [[ "$out" != *"not installed" ]]; then
+    echo >&2 "$out"
+    exit 1
+fi
+
+# Finally actually do the installation
+echo "Installing package $name using pip"
+exec pip install $pip_install_flags .
diff --git a/build/pkgs/alabaster/package-version.txt b/build/pkgs/alabaster/package-version.txt
@@ -1 +1 @@
-0.7.8
+0.7.8.p0
diff --git a/build/pkgs/appnope/package-version.txt b/build/pkgs/appnope/package-version.txt
@@ -1 +1 @@
-0.1.0
+0.1.0.p0
diff --git a/build/pkgs/babel/package-version.txt b/build/pkgs/babel/package-version.txt
@@ -1 +1 @@
-2.3.4
+2.3.4.p0
diff --git a/build/pkgs/backports_abc/package-version.txt b/build/pkgs/backports_abc/package-version.txt
@@ -1 +1 @@
-0.4
+0.4.p0
diff --git a/build/pkgs/backports_shutil_get_terminal_size/package-version.txt b/build/pkgs/backports_shutil_get_terminal_size/package-version.txt
@@ -1 +1 @@
-1.0.0.p0
+1.0.0.p1
diff --git a/build/pkgs/backports_ssl_match_hostname/package-version.txt b/build/pkgs/backports_ssl_match_hostname/package-version.txt
@@ -1 +1 @@
-3.5.0.1
+3.5.0.1.p0
diff --git a/build/pkgs/certifi/package-version.txt b/build/pkgs/certifi/package-version.txt
@@ -1 +1 @@
-2016.2.28
+2016.2.28.p0
diff --git a/build/pkgs/cvxopt/dependencies b/build/pkgs/cvxopt/dependencies
@@ -1,4 +1,4 @@
-numpy $(BLAS) cephes gsl glpk | pkgconfig pip matplotlib
+$(PYTHON) numpy $(BLAS) cephes gsl glpk | pkgconfig pip matplotlib
 
 matplotlib is needed to test cvxopt (i.e., if SAGE_CHECK=yes). See #12742.
 

diff --git a/build/pkgs/cvxopt/package-version.txt b/build/pkgs/cvxopt/package-version.txt
@@ -1 +1 @@
-1.1.8.p1
+1.1.8.p2
diff --git a/build/pkgs/cycler/package-version.txt b/build/pkgs/cycler/package-version.txt
@@ -1 +1 @@
-0.10.0
+0.10.0.p0
diff --git a/build/pkgs/cython/package-version.txt b/build/pkgs/cython/package-version.txt
@@ -1 +1 @@
-0.24.1.p1
+0.24.1.p2
diff --git a/build/pkgs/dateutil/package-version.txt b/build/pkgs/dateutil/package-version.txt
@@ -1 +1 @@
-2.2
+2.2.p0
diff --git a/build/pkgs/decorator/package-version.txt b/build/pkgs/decorator/package-version.txt
@@ -1 +1 @@
-4.0.6
+4.0.6.p0
diff --git a/build/pkgs/docutils/package-version.txt b/build/pkgs/docutils/package-version.txt
@@ -1 +1 @@
-0.12
+0.12.p0
diff --git a/build/pkgs/dot2tex/package-version.txt b/build/pkgs/dot2tex/package-version.txt
@@ -1 +1 @@
-2.9.0.p0
+2.9.0.p1
diff --git a/build/pkgs/flask/package-version.txt b/build/pkgs/flask/package-version.txt
@@ -1 +1 @@
-0.10.1
+0.10.1.p0
diff --git a/build/pkgs/flask_autoindex/package-version.txt b/build/pkgs/flask_autoindex/package-version.txt
@@ -1 +1 @@
-0.6
+0.6.p0
diff --git a/build/pkgs/flask_babel/package-version.txt b/build/pkgs/flask_babel/package-version.txt
@@ -1 +1 @@
-0.9
+0.9.p0
diff --git a/build/pkgs/flask_oldsessions/package-version.txt b/build/pkgs/flask_oldsessions/package-version.txt
@@ -1 +1 @@
-0.10
+0.10.p0
diff --git a/build/pkgs/flask_openid/package-version.txt b/build/pkgs/flask_openid/package-version.txt
@@ -1 +1 @@
-1.2.5
+1.2.5.p0
diff --git a/build/pkgs/flask_silk/package-version.txt b/build/pkgs/flask_silk/package-version.txt
@@ -1 +1 @@
-0.2
+0.2.p0
diff --git a/build/pkgs/functools32/package-version.txt b/build/pkgs/functools32/package-version.txt
@@ -1 +1 @@
-3.2.3-2
+3.2.3-2.p0
diff --git a/build/pkgs/future/package-version.txt b/build/pkgs/future/package-version.txt
@@ -1 +1 @@
-0.15.2
+0.15.2.p0
diff --git a/build/pkgs/giacpy/package-version.txt b/build/pkgs/giacpy/package-version.txt
@@ -1 +1 @@
-0.5.6
+0.5.6.p0
diff --git a/build/pkgs/git_trac/package-version.txt b/build/pkgs/git_trac/package-version.txt
@@ -1 +1 @@
-20160625
+20160625.p0
diff --git a/build/pkgs/imagesize/package-version.txt b/build/pkgs/imagesize/package-version.txt
@@ -1 +1 @@
-0.7.1
+0.7.1.p0
diff --git a/build/pkgs/ipykernel/package-version.txt b/build/pkgs/ipykernel/package-version.txt
@@ -1 +1 @@
-4.3.1
+4.3.1.p0
diff --git a/build/pkgs/ipython/package-version.txt b/build/pkgs/ipython/package-version.txt
@@ -1 +1 @@
-5.0.0
+5.0.0.p0
diff --git a/build/pkgs/ipython_genutils/package-version.txt b/build/pkgs/ipython_genutils/package-version.txt
@@ -1 +1 @@
-0.1.0
+0.1.0.p0
diff --git a/build/pkgs/ipywidgets/package-version.txt b/build/pkgs/ipywidgets/package-version.txt
@@ -1 +1 @@
-5.2.2.p0
+5.2.2.p1
diff --git a/build/pkgs/itsdangerous/package-version.txt b/build/pkgs/itsdangerous/package-version.txt
@@ -1 +1 @@
-0.24
+0.24.p0
diff --git a/build/pkgs/jinja2/package-version.txt b/build/pkgs/jinja2/package-version.txt
@@ -1 +1 @@
-2.8
+2.8.p0
diff --git a/build/pkgs/jsonschema/package-version.txt b/build/pkgs/jsonschema/package-version.txt
@@ -1 +1 @@
-2.5.1
+2.5.1.p0
diff --git a/build/pkgs/jupyter_client/package-version.txt b/build/pkgs/jupyter_client/package-version.txt
@@ -1 +1 @@
-4.3.0
+4.3.0.p0
diff --git a/build/pkgs/jupyter_core/package-version.txt b/build/pkgs/jupyter_core/package-version.txt
@@ -1 +1 @@
-4.1.0
+4.1.0.p0
diff --git a/build/pkgs/markupsafe/package-version.txt b/build/pkgs/markupsafe/package-version.txt
@@ -1 +1 @@
-0.23
+0.23.p0
diff --git a/build/pkgs/matplotlib/package-version.txt b/build/pkgs/matplotlib/package-version.txt
@@ -1 +1 @@
-1.5.1
+1.5.1.p0
diff --git a/build/pkgs/mistune/package-version.txt b/build/pkgs/mistune/package-version.txt
@@ -1 +1 @@
-0.7.3
+0.7.3.p0
diff --git a/build/pkgs/mpmath/package-version.txt b/build/pkgs/mpmath/package-version.txt
@@ -1 +1 @@
-0.19
+0.19.p0
diff --git a/build/pkgs/nbconvert/package-version.txt b/build/pkgs/nbconvert/package-version.txt
@@ -1 +1 @@
-4.2.0
+4.2.0.p0
diff --git a/build/pkgs/nbformat/package-version.txt b/build/pkgs/nbformat/package-version.txt
@@ -1 +1 @@
-4.0.1
+4.0.1.p0
diff --git a/build/pkgs/networkx/package-version.txt b/build/pkgs/networkx/package-version.txt
@@ -1 +1 @@
-1.11
+1.11.p0
diff --git a/build/pkgs/nose/package-version.txt b/build/pkgs/nose/package-version.txt
@@ -1 +1 @@
-1.3.3
+1.3.3.p0
diff --git a/build/pkgs/notebook/package-version.txt b/build/pkgs/notebook/package-version.txt
@@ -1 +1 @@
-4.2.1
+4.2.1.p0
diff --git a/build/pkgs/ore_algebra/package-version.txt b/build/pkgs/ore_algebra/package-version.txt
@@ -1 +1 @@
-0.2
+0.2.p0
diff --git a/build/pkgs/pari_jupyter/package-version.txt b/build/pkgs/pari_jupyter/package-version.txt
@@ -1 +1 @@
-1.1.0
+1.1.0.p0
diff --git a/build/pkgs/pathlib2/package-version.txt b/build/pkgs/pathlib2/package-version.txt
@@ -1 +1 @@
-2.1.0
+2.1.0.p0
diff --git a/build/pkgs/pathpy/package-version.txt b/build/pkgs/pathpy/package-version.txt
@@ -1 +1 @@
-7.1
+7.1.p0
diff --git a/build/pkgs/pexpect/package-version.txt b/build/pkgs/pexpect/package-version.txt
@@ -1 +1 @@
-4.1.0
+4.1.0.p0
diff --git a/build/pkgs/pickleshare/package-version.txt b/build/pkgs/pickleshare/package-version.txt
@@ -1 +1 @@
-0.7.2
+0.7.2.p0
diff --git a/build/pkgs/pip/package-version.txt b/build/pkgs/pip/package-version.txt
@@ -1 +1 @@
-8.1.2.p0
+8.1.2.p1
diff --git a/build/pkgs/pip/spkg-install b/build/pkgs/pip/spkg-install
@@ -15,4 +15,4 @@ done
 # pip can install itself!
 # need to use --upgrade or else pip, which is importing itself, will think
 # itself is already installed
-python -m $PIP_INSTALL --upgrade .
+python -m pip install --verbose --no-index --upgrade .
diff --git a/build/pkgs/pkgconfig/package-version.txt b/build/pkgs/pkgconfig/package-version.txt
@@ -1 +1 @@
-1.1.0
+1.1.0.p0
diff --git a/build/pkgs/prompt_toolkit/dependencies b/build/pkgs/prompt_toolkit/dependencies
@@ -1,4 +1,4 @@
-$(PYTHON) setuptools six wcwidth
+$(PYTHON) six wcwidth | pip
 
 ----------
 All lines of this file are ignored except the first.

diff --git a/build/pkgs/prompt_toolkit/package-version.txt b/build/pkgs/prompt_toolkit/package-version.txt
@@ -1 +1 @@
-1.0.3
+1.0.3.p0
diff --git a/build/pkgs/psutil/package-version.txt b/build/pkgs/psutil/package-version.txt
@@ -1 +1 @@
-4.3.1
+4.3.1.p0
diff --git a/build/pkgs/ptyprocess/package-version.txt b/build/pkgs/ptyprocess/package-version.txt
@@ -1 +1 @@
-0.5.1
+0.5.1.p0
diff --git a/build/pkgs/pycrypto/package-version.txt b/build/pkgs/pycrypto/package-version.txt
@@ -1 +1 @@
-2.6.1.p1
+2.6.1.p2
diff --git a/build/pkgs/pygments/package-version.txt b/build/pkgs/pygments/package-version.txt
@@ -1 +1 @@
-2.1.3.p0
+2.1.3.p1
diff --git a/build/pkgs/pyparsing/package-version.txt b/build/pkgs/pyparsing/package-version.txt
@@ -1 +1 @@
-2.1.5
+2.1.5.p0
diff --git a/build/pkgs/python_igraph/package-version.txt b/build/pkgs/python_igraph/package-version.txt
@@ -1 +1 @@
-0.7.0
+0.7.0.p0
diff --git a/build/pkgs/python_openid/package-version.txt b/build/pkgs/python_openid/package-version.txt
@@ -1 +1 @@
-2.2.5
+2.2.5.p0
diff --git a/build/pkgs/pytz/package-version.txt b/build/pkgs/pytz/package-version.txt
@@ -1 +1 @@
-2016.4
+2016.4.p0
diff --git a/build/pkgs/pyx/dependencies b/build/pkgs/pyx/dependencies
@@ -1,4 +1,4 @@
-$(PYTHON)
+$(PYTHON) | pip
 
 ----------
 All lines of this file are ignored except the first.

diff --git a/build/pkgs/pyx/package-version.txt b/build/pkgs/pyx/package-version.txt
@@ -1 +1 @@
-0.12.1
+0.12.1.p0
diff --git a/build/pkgs/pyzmq/package-version.txt b/build/pkgs/pyzmq/package-version.txt
@@ -1 +1 @@
-15.3.0
+15.3.0.p0
diff --git a/build/pkgs/rpy2/package-version.txt b/build/pkgs/rpy2/package-version.txt
@@ -1 +1 @@
-2.8.2
+2.8.2.p0
diff --git a/build/pkgs/sagenb_export/dependencies b/build/pkgs/sagenb_export/dependencies
@@ -1,4 +1,4 @@
-nbconvert ipython six
+$(PYTHON) nbconvert ipython six | pip
 
 ----------
 All lines of this file are ignored except the first.

diff --git a/build/pkgs/sagenb_export/package-version.txt b/build/pkgs/sagenb_export/package-version.txt
@@ -1 +1 @@
-2.0
+2.0.p0
diff --git a/build/pkgs/scipy/package-version.txt b/build/pkgs/scipy/package-version.txt
@@ -1 +1 @@
-0.17.1
+0.17.1.p0
diff --git a/build/pkgs/setuptools_scm/package-version.txt b/build/pkgs/setuptools_scm/package-version.txt
@@ -1 +1 @@
-1.11.1
+1.11.1.p0
diff --git a/build/pkgs/simplegeneric/package-version.txt b/build/pkgs/simplegeneric/package-version.txt
@@ -1 +1 @@
-0.8.1
+0.8.1.p0
diff --git a/build/pkgs/singledispatch/package-version.txt b/build/pkgs/singledispatch/package-version.txt
@@ -1 +1 @@
-3.4.0.3
+3.4.0.3.p0
diff --git a/build/pkgs/six/package-version.txt b/build/pkgs/six/package-version.txt
@@ -1 +1 @@
-1.10.0
+1.10.0.p0
diff --git a/build/pkgs/snowballstemmer/package-version.txt b/build/pkgs/snowballstemmer/package-version.txt
@@ -1 +1 @@
-1.2.1
+1.2.1.p0
diff --git a/build/pkgs/speaklater/package-version.txt b/build/pkgs/speaklater/package-version.txt
@@ -1 +1 @@
-1.3
+1.3.p0
diff --git a/build/pkgs/sphinx/package-version.txt b/build/pkgs/sphinx/package-version.txt
@@ -1 +1 @@
-1.4.4
+1.4.4.p0
diff --git a/build/pkgs/sympy/package-version.txt b/build/pkgs/sympy/package-version.txt
@@ -1 +1 @@
-1.0.p0
+1.0.p1
diff --git a/build/pkgs/tornado/package-version.txt b/build/pkgs/tornado/package-version.txt
@@ -1 +1 @@
-4.3
+4.3.p0
diff --git a/build/pkgs/traitlets/package-version.txt b/build/pkgs/traitlets/package-version.txt
@@ -1 +1 @@
-4.2.2
+4.2.2.p0
diff --git a/build/pkgs/twisted/package-version.txt b/build/pkgs/twisted/package-version.txt
@@ -1 +1 @@
-16.3.0
+16.3.0.p0
diff --git a/build/pkgs/vcversioner/package-version.txt b/build/pkgs/vcversioner/package-version.txt
@@ -1 +1 @@
-2.16.0.0
+2.16.0.0.p0
diff --git a/build/pkgs/wcwidth/package-version.txt b/build/pkgs/wcwidth/package-version.txt
@@ -1 +1 @@
-0.1.7
+0.1.7.p0
diff --git a/build/pkgs/werkzeug/package-version.txt b/build/pkgs/werkzeug/package-version.txt
@@ -1 +1 @@
-0.11.10
+0.11.10.p0
diff --git a/build/pkgs/widgetsnbextension/package-version.txt b/build/pkgs/widgetsnbextension/package-version.txt
@@ -1 +1 @@
-1.2.6
+1.2.6.p0
diff --git a/build/pkgs/zope_interface/package-version.txt b/build/pkgs/zope_interface/package-version.txt
@@ -1 +1 @@
-4.2.0
+4.2.0.p0
diff --git a/src/bin/sage-env b/src/bin/sage-env
@@ -654,15 +654,7 @@ if [ "${MAKEFLAGS-__unset__}" != "__unset__" ]; then
 fi
 export MAKE
 
-# Default arguments for all packages installed with `pip install`
-# --ignore-installed : Force pip to re-install package even if it thinks it's
-#                      already installed (for which it sometimes gets false
-#                      positives for partially-installed packages).
-# --verbose          : Display the output when running setup.py.
-# --no-deps          : Don't install runtime dependencies from PyPI.
-# --no-index         : Don't look at the package index.
-#                      This also disables pip's version self-check.
-export PIP_INSTALL="pip install --ignore-installed --verbose --no-deps --no-index"
+export PIP_INSTALL="sage-pip-install"
 
 # When building documentation, use MathJax by default. To turn it off,
 # set SAGE_DOC_MATHJAX to be "no" or "False".