Merge #33740

sagemath · May 14, 2022 · 765dff7 · 765dff7
2 parents 888d18e + 87f360c
commit 765dff7
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diff --git a/.github/workflows/ci-conda.yml b/.github/workflows/ci-conda.yml
@@ -43,15 +43,8 @@ jobs:
           bash ~/miniconda.sh -b -p $HOME/miniconda
           echo "CONDA=$HOME/miniconda" >> $GITHUB_ENV
 
-      - name: Install bootstrap prerequisites
-        run: |
-          export PATH="$(pwd)/build/bin:$PATH"
-          SYSTEM=$(sage-guess-package-system)
-          eval $(sage-print-system-package-command $SYSTEM --sudo install $(sage-get-system-packages $SYSTEM _bootstrap))
-
-      # Create conda environment file
-      - name: Bootstrap
-        run: ./bootstrap
+      - name: Create conda environment files
+        run: ./bootstrap-conda
 
       - name: Cache conda packages
         uses: actions/cache@v2
@@ -80,6 +73,7 @@ jobs:
         shell: bash -l {0}
         continue-on-error: true
         run: |
+          ./bootstrap
           echo "::add-matcher::.github/workflows/configure-systempackage-problem-matcher.json"
           ./configure --enable-build-as-root --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX $(for pkg in $(./sage -package list :standard: --has-file spkg-configure.m4 --has-file distros/conda.txt); do echo --with-system-$pkg=force; done)
           echo "::remove-matcher owner=configure-system-package-warning::"
@@ -88,8 +82,8 @@ jobs:
       - name: Build
         shell: bash -l {0}
         run: |
-          pip install --no-build-isolation -v -v -e pkgs/sage-conf pkgs/sage-setup 
-          pip install --no-build-isolation -v -v -e src
+          pip install --no-build-isolation -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup
+          pip install --no-build-isolation -v -v -e ./src
         env:
           SAGE_NUM_THREADS: 2
 

diff --git a/.gitignore b/.gitignore
@@ -23,6 +23,7 @@
 /environment.yml
 /environment-optional.yml
 /src/environment.yml
+/src/environment-dev.yml
 /src/environment-optional.yml
 
 /src/setup.cfg

diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -19,4 +19,8 @@
         "src"
     ],
     "python.testing.unittestEnabled": false,
+    "cSpell.words": [
+        "Conda",
+        "Cython"
+    ],
 }
diff --git a/Makefile b/Makefile
@@ -171,6 +171,7 @@ bootstrap-clean:
 	rm -f src/doc/en/reference/repl/*.txt
 	rm -f environment.yml
 	rm -f src/environment.yml
+	rm -f src/environment-dev.yml
 	rm -f environment-optional.yml
 	rm -f src/environment-optional.yml
 	rm -f src/Pipfile

diff --git a/bootstrap b/bootstrap
@@ -158,6 +158,7 @@ SAGE_SPKG_FINALIZE([$pkgname], [$pkgtype], [$SPKG_SOURCE], [$SPKG_TREE_VAR])"
     # ONLY stderr, and to re-output the results back to stderr leaving
     # stdout alone. Basically we swap the two descriptors using a
     # third, filter, and then swap them back.
+    ./bootstrap-conda && \
     src/doc/bootstrap && \
     install_config_rpath && \
     aclocal -I m4 && \

diff --git a/bootstrap-conda b/bootstrap-conda
@@ -0,0 +1,78 @@
+#!/usr/bin/env bash
+
+########################################################################
+# Generate auto-generated conda environment files
+#########################################################################
+
+STRIP_COMMENTS="sed s/#.*//;"
+RECOMMENDED_SPKG_PATTERN="@(_recommended$(for a in $(head -n 1 build/pkgs/_recommended/dependencies); do echo -n "|"$a; done))"
+
+BOOTSTRAP_PACKAGES=$(echo $(${STRIP_COMMENTS} build/pkgs/_bootstrap/distros/conda.txt))
+SYSTEM_PACKAGES=
+OPTIONAL_SYSTEM_PACKAGES=
+SAGELIB_SYSTEM_PACKAGES=
+SAGELIB_OPTIONAL_SYSTEM_PACKAGES=
+RECOMMENDED_SYSTEM_PACKAGES=
+for PKG_BASE in $(./sage --package list --has-file distros/conda.txt); do
+    PKG_SCRIPTS=build/pkgs/$PKG_BASE
+    SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/distros/conda.txt
+    PKG_TYPE=$(cat $PKG_SCRIPTS/type)
+    PKG_SYSTEM_PACKAGES=$(echo $(${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE))
+    if [ -n "PKG_SYSTEM_PACKAGES" ]; then
+        if [ -f $PKG_SCRIPTS/spkg-configure.m4 ]; then
+            case "$PKG_BASE:$PKG_TYPE" in
+                *:standard)
+                    SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
+                $RECOMMENDED_SPKG_PATTERN:*)
+                    RECOMMENDED_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
+                *)
+                    OPTIONAL_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
+            esac
+        else
+            case "$PKG_TYPE" in
+                standard)
+                    SAGELIB_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
+                *)
+                    SAGELIB_OPTIONAL_SYSTEM_PACKAGES+=" $PKG_SYSTEM_PACKAGES"
+                    ;;
+            esac
+        fi
+    fi
+done
+echo >&2 $0:$LINENO: generate conda enviroment files
+echo "name: sage-build" >  environment.yml
+echo "channels:"        >> environment.yml
+echo "  - conda-forge"  >> environment.yml
+echo "  - nodefaults"   >> environment.yml
+echo "dependencies:"    >> environment.yml
+for pkg in $SYSTEM_PACKAGES; do
+    echo "  - $pkg" >> environment.yml
+done
+echo "  # Packages needed for ./bootstrap" >> environment.yml
+for pkg in $BOOTSTRAP_PACKAGES; do
+    echo "  - $pkg" >> environment.yml
+done
+sed 's/name: sage-build/name: sage/' environment.yml > src/environment.yml
+for pkg in $SAGELIB_SYSTEM_PACKAGES; do
+    echo "  - $pkg" >> src/environment.yml
+done
+sed 's/name: sage/name: sage-dev/' src/environment.yml > src/environment-dev.yml
+echo "  # Additional dev tools" >> src/environment-dev.yml
+echo "  - openssh" >> src/environment-dev.yml
+echo "  - pycodestyle" >> src/environment-dev.yml
+echo "  - pytest" >> src/environment-dev.yml
+
+cp environment.yml environment-optional.yml
+    echo "  # optional packages" >> environment-optional.yml
+for pkg in $OPTIONAL_SYSTEM_PACKAGES; do
+    echo "  - $pkg" >> environment-optional.yml
+    done
+cp src/environment.yml src/environment-optional.yml
+    echo "  # optional packages" >> src/environment-optional.yml
+for pkg in $OPTIONAL_SYSTEM_PACKAGES $SAGELIB_OPTIONAL_SYSTEM_PACKAGES; do
+    echo "  - $pkg" >> src/environment-optional.yml
+done
diff --git a/build/pkgs/jupyter_sphinx/distros/conda.txt b/build/pkgs/jupyter_sphinx/distros/conda.txt
@@ -0,0 +1 @@
+jupyter_sphinx
diff --git a/src/doc/bootstrap b/src/doc/bootstrap
@@ -27,7 +27,7 @@ shopt -s extglob
 
 RECOMMENDED_SPKG_PATTERN="@(_recommended$(for a in $(head -n 1 build/pkgs/_recommended/dependencies); do echo -n "|"$a; done))"
 
-for SYSTEM in arch debian fedora cygwin homebrew conda; do
+for SYSTEM in arch debian fedora cygwin homebrew; do
     SYSTEM_PACKAGES=
     OPTIONAL_SYSTEM_PACKAGES=
     SAGELIB_SYSTEM_PACKAGES=
@@ -63,40 +63,13 @@ for SYSTEM in arch debian fedora cygwin homebrew conda; do
                     fi
                 fi
     done
-    if [ "${SYSTEM}" = "conda" ]; then
-        if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
-            echo >&2 $0:$LINENO: installing environment.yml, environment-optional.yml, src/environment.yml and src/environment-optional.yml
-        fi
-        echo "name: sage-build" >  environment.yml
-        echo "channels:"        >> environment.yml
-        echo "  - conda-forge"  >> environment.yml
-        echo "  - nodefaults"   >> environment.yml
-        echo "dependencies:"    >> environment.yml
-        for pkg in $SYSTEM_PACKAGES; do
-            echo "  - $pkg" >> environment.yml
-        done
-        sed 's/name: sage-build/name: sage/' environment.yml > src/environment.yml
-        for pkg in $SAGELIB_SYSTEM_PACKAGES; do
-            echo "  - $pkg" >> src/environment.yml
-        done
-        cp environment.yml environment-optional.yml
-            echo "  # optional packages" >> environment-optional.yml
-        for pkg in $OPTIONAL_SYSTEM_PACKAGES; do
-            echo "  - $pkg" >> environment-optional.yml
-            done
-        cp src/environment.yml src/environment-optional.yml
-            echo "  # optional packages" >> src/environment-optional.yml
-        for pkg in $OPTIONAL_SYSTEM_PACKAGES $SAGELIB_OPTIONAL_SYSTEM_PACKAGES; do
-            echo "  - $pkg" >> src/environment-optional.yml
-        done
-    else
-        if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
-            echo >&2 $0:$LINENO: installing "$OUTPUT_DIR"/$SYSTEM"*.txt"
-        fi
-        echo "$(sage-print-system-package-command $SYSTEM --prompt --sudo install $(echo $(echo $SYSTEM_PACKAGES | xargs -n 1 echo | sort | uniq)))" > "$OUTPUT_DIR"/$SYSTEM.txt
-        echo "$(sage-print-system-package-command $SYSTEM --prompt --sudo install $(echo $(echo $OPTIONAL_SYSTEM_PACKAGES | xargs -n 1 echo | sort | uniq)))" > "$OUTPUT_DIR"/$SYSTEM-optional.txt
-        echo "$(sage-print-system-package-command $SYSTEM --prompt --sudo install $(echo $(echo $RECOMMENDED_SYSTEM_PACKAGES | xargs -n 1 echo | sort | uniq)))" > "$OUTPUT_DIR"/$SYSTEM-recommended.txt
+
+    if [ "${BOOTSTRAP_QUIET}" = "no" ]; then
+        echo >&2 $0:$LINENO: installing "$OUTPUT_DIR"/$SYSTEM"*.txt"
     fi
+    echo "$(sage-print-system-package-command $SYSTEM --prompt --sudo install $(echo $(echo $SYSTEM_PACKAGES | xargs -n 1 echo | sort | uniq)))" > "$OUTPUT_DIR"/$SYSTEM.txt
+    echo "$(sage-print-system-package-command $SYSTEM --prompt --sudo install $(echo $(echo $OPTIONAL_SYSTEM_PACKAGES | xargs -n 1 echo | sort | uniq)))" > "$OUTPUT_DIR"/$SYSTEM-optional.txt
+    echo "$(sage-print-system-package-command $SYSTEM --prompt --sudo install $(echo $(echo $RECOMMENDED_SYSTEM_PACKAGES | xargs -n 1 echo | sort | uniq)))" > "$OUTPUT_DIR"/$SYSTEM-recommended.txt
 done
 
 OUTPUT_DIR="src/doc/en/reference/spkg"

diff --git a/src/doc/en/installation/conda.rst b/src/doc/en/installation/conda.rst
@@ -61,25 +61,22 @@ To use Sage from there,
 Using conda to provide system packages for the Sage distribution
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-If Conda is installed (check by typing ``conda info``), there are two ways to
-prepare for installing SageMath from source:
+If Conda is installed (check by typing ``conda info``), one can install SageMath
+from source as follows:
 
   - If you are using a git checkout::
 
-      $ ./bootstrap
+      $ ./bootstrap-conda
 
-  - Create a new empty environment and activate::
+  - Create a new conda environment including all standard packages
+    recognized by sage, and activate it::
 
-      $ conda create -n sage-build
+      $ conda env create --file environment.yml --name sage-build
       $ conda activate sage-build
 
-  - Install standard packages recognized by sage's ``spkg-configure`` mechanism::
-
-      $ conda env update --file environment.yml -n sage-build
-
-  - Or install all standard and optional packages recognized by sage::
-
-      $ conda env update --file environment-optional.yml -n sage-build
+    Alternatively, use ``environment-optional.yml`` in place of
+    ``environment.yml`` to create an environment with all standard and optional
+    packages recognized by sage.
 
   - Then the SageMath distribution will be built using the compilers provided by Conda
     and using many packages installed by Conda::
@@ -110,38 +107,34 @@ Here we assume that you are using a git checkout.
 
       $ export SAGE_NUM_THREADS=24
 
-  - As a recommended step, install the ``mamba`` package manager.  If
+  - As a recommended step, install the ``mamba`` package manager. If
     you skip this step, replace ``mamba`` by ``conda`` in the
     following steps::
 
       $ conda install mamba
 
-  - Create and activate a new conda environment that provides the
-    bootstrapping prerequisites. You can replace 3.9 by another Python
-    version::
-
-      $ mamba create -n sage-build python=3.9 \
-            gettext autoconf automake libtool pkg-config
-      $ conda activate sage-build
-
-  - Run ``bootstrap``; this generates the files ``src/environment*.yml`` used
+  - Generate the conda environment files ``src/environment*.yml`` used
     in the next step::
 
-      $ ./bootstrap
-
-  - Populate the conda environment with the dependencies of Sage::
+      $ ./bootstrap-conda
 
-      $ mamba env update -n sage-build -f src/environment.yml  # alternatively, use
+  - Create and activate a new conda environment with the dependencies of Sage
+    and a few additional developer tools::
 
-    Alternatively, you can use ``src/environment-optional.yml``, which will
-    install some additional packages.
+      $ mamba env create --file src/environment-dev.yml --name sage-dev
+      $ conda activate sage-dev
 
-  - Activate the conda environment again::
+    Alternatively, you can use ``src/environment.yml`` or
+    ``src/environment-optional.yml``, which will only install standard
+    (and optional) packages without any additional developer tools.
 
-      $ conda activate sage-build
+    By default, the most recent version of Python supported by Sage is
+    installed. You can use the additional option ``python=3.9`` in the above
+    ``env create`` command to select another Python version (here 3.9). 
 
   - Run the ``configure`` script::
 
+      $ ./bootstrap
       $ ./configure --with-python=$CONDA_PREFIX/bin/python             \
                     --prefix=$CONDA_PREFIX                             \
                     $(for pkg in $(./sage -package list :standard:     \
@@ -150,20 +143,17 @@ Here we assume that you are using a git checkout.
                           echo --with-system-$pkg=force;               \
                       done)
 
-  - Install the build prerequisites of the Sage library::
-
-      $ pip install --no-build-isolation -v -v --editable pkgs/sage-conf pkgs/sage-setup
-
-  - Install the Sage library::
+  - Install the build prerequisites and the Sage library::
 
-      $ pip install --no-build-isolation -v -v --editable src
+      $ pip install --no-build-isolation -v -v --editable ./pkgs/sage-conf ./pkgs/sage-setup
+      $ pip install --no-build-isolation -v -v --editable ./src
 
   - Verify that Sage has been installed::
 
       $ sage -c 'print(version())'
       SageMath version 9.6.beta5, Release Date: 2022-03-12
 
-Note that ``make`` is not used at all.  All dependencies
+Note that ``make`` is not used at all. All dependencies
 (including all Python packages) are provided by conda.
 
 Thus, you will get a working version of Sage much faster.  However,
@@ -175,6 +165,6 @@ library is installed in editable mode.  This means that when you only
 edit Python files, there is no need to rebuild the library; it
 suffices to restart Sage.
 
-After editing any Cython files, rebuild by repeating the command::
+After editing any Cython files, rebuild the Sage library using::
 
   $ pip install --no-build-isolation -v -v --editable src