Merge pull request #1 from dimpase/wwp

this is a rebase over #34985

.devcontainer/devcontainer.json

@@ -0,0 +1,35 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.2/containers/debian
+{
+	"name": "Conda",
+	"image": "mcr.microsoft.com/vscode/devcontainers/base:0-bullseye",
+
+	// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
+	"remoteUser": "vscode",
+
+	// Setup conda environment
+	"onCreateCommand": ".devcontainer/onCreate-conda.sh",
+
+	// Install additional features.
+	"features": {
+		// For config options, see https://github.com/devcontainers/features/tree/main/src/conda
+		"ghcr.io/devcontainers/features/conda": {
+            "version": "latest",
+			"addCondaForge": "true"
+        }
+	},
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"guyskk.language-cython",
+				"ms-python.isort",
+				"ms-toolsai.jupyter",
+				"ms-python.vscode-pylance",
+				"ms-python.pylint",
+				"ms-python.python",
+				"lextudio.restructuredtext",
+				"trond-snekvik.simple-rst"
+			]
+		}
+	}
+}

.devcontainer/onCreate-conda.sh

@@ -0,0 +1,14 @@
+# Do not keep running on errors
+set -e
+
+# Create conda environment
+./bootstrap-conda
+conda install mamba -n base -c conda-forge -y
+mamba env create --file src/environment-dev.yml || mamba env update --file src/environment-dev.yml
+conda init bash
+
+# Build sage
+conda run -n sage-dev ./bootstrap
+conda run -n sage-dev ./configure --with-python=/opt/conda/envs/sage-dev/bin/python --prefix=/opt/conda/envs/sage-dev
+conda run -n sage-dev pip install --no-build-isolation -v -v -e ./pkgs/sage-conf ./pkgs/sage-setup 
+conda run -n sage-dev pip install --no-build-isolation -v -v -e ./src

.github/workflows/ci-cygwin-standard.yml

@@ -59,13 +59,11 @@ jobs:
     needs: [cygwin-stage-i-a, cygwin-stage-i-b]
 
   cygwin-stage-ii-e:
-    env:
-      STAGE: ii-e
-      PREVIOUS_STAGES: i-*
-      TARGETS: threejs tachyon pillow jmol m4rie sympy lrcalc lcalc symmetrica cliquer libbraiding planarity rw elliptic_curves combinatorial_designs sympow
-      LOCAL_ARTIFACT_NAME: sage-local-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
-      LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-cygwin-${{ matrix.pkgs }}
-
+    uses: ./.github/workflows/cygwin.yml
+    with:
+      stage: ii-e
+      previous_stages: i-*
+      targets: threejs tachyon pillow jmol m4rie sympy lrcalc lcalc symmetrica cliquer libbraiding planarity rw elliptic_curves combinatorial_designs sympow
     needs: [cygwin-stage-i-a, cygwin-stage-i-b]
 
 ############################################## stage-iii ##########################################

.github/workflows/ci-linux.yml

@@ -162,41 +162,3 @@ jobs:
           ["maximal"]
       docker_targets: "with-targets-optional"
       targets_optional: '$(echo $(export PATH=build/bin:$PATH && sage-package list :experimental: --has-file "spkg-install.in|spkg-install|requirements.txt" --no-file "huge|has_nonfree_dependencies" | grep -v sagemath_doc | grep ^[p-z]))'
-
-  local-ubuntu:
-
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      max-parallel: 1
-      matrix:
-        tox_system_factor: [conda-forge-ubuntu]
-        tox_packages_factor: [minimal, standard, environment, environment-optional]
-    env:
-      TOX_ENV: local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
-      LOGS_ARTIFACT_NAME: logs-commit-${{ github.sha }}-tox-local-${{ matrix.tox_system_factor }}-${{ matrix.tox_packages_factor }}
-    steps:
-      - uses: actions/checkout@v3
-      - name: Install test prerequisites
-        run: |
-          sudo DEBIAN_FRONTEND=noninteractive apt-get update
-          sudo DEBIAN_FRONTEND=noninteractive apt-get install tox
-      - name: Build and test with tox
-        # We use a high parallelization on purpose in order to catch possible parallelization bugs in the build scripts.
-        # For doctesting, we use a lower parallelization to avoid timeouts.
-        run: |
-          MAKE="make -j12" tox -e $TOX_ENV -- SAGE_NUM_THREADS=4 $TARGETS
-      - name: Prepare logs artifact
-        run: |
-          mkdir -p "artifacts/$LOGS_ARTIFACT_NAME"; cp -r .tox/*/log "artifacts/$LOGS_ARTIFACT_NAME"
-        if: always()
-      - uses: actions/upload-artifact@v3
-        with:
-          path: artifacts
-          name: ${{ env.LOGS_ARTIFACT_NAME }}
-        if: always()
-      - name: Print out logs for immediate inspection
-        # and markup the output with GitHub Actions logging commands
-        run: |
-          .github/workflows/scan-logs.sh "artifacts/$LOGS_ARTIFACT_NAME"
-        if: always()

.gitignore

@@ -221,9 +221,6 @@ src/ENV/
 src/env.bak/
 src/venv.bak/
 
-# devcontainer
-/.devcontainer/devcontainer.json
-
 # mypy
 **/.mypy_cache/
 

src/doc/en/developer/portability_testing.rst

@@ -1164,23 +1164,7 @@ provides sample ``devcontainer.json`` configuration files
 <https://github.com/sagemath/sage/tree/develop/.devcontainer/>`_ for this
 purpose.
 
-To get started, symlink (or copy) one of the sample files to
-``$SAGE_ROOT/.devcontainer/devcontainer.json``. For example, choose
-`$SAGE_ROOT/.devcontainer/portability-ubuntu-jammy-standard/devcontainer.json
-<https://github.com/sagemath/sage/tree/develop/.devcontainer/portability-ubuntu-jammy-standard/devcontainer.json>`_, which uses the Docker image based on ``ubuntu-jammy-standard``,
-the most recent
-development version of Sage (``dev`` tag), and a full installation of
-the Sage distribution (``with-targets``).
-
-In macOS for example, you can do this using the shell as follows::
-
-  [mkoeppe@sage sage] $ (cd .devcontainer && ln -s portability-ubuntu-jammy-standard/devcontainer.json .)
-
-Now start VS Code::
-
-  [mkoeppe@sage sage] $ code .
-
-Then VS Code may prompt you whether you would like to open the current
+If you open the sage folder in VS Code, it may prompt you whether you would like to open the current
 directory in the dev container (yes).  If it does not, use the command palette
 (:kbd:`Ctrl` + :kbd:`Shift` + :kbd:`P`), enter the command "Remote-Containers:
 Reopen Folder in Container" , and hit :kbd:`Enter`.
@@ -1190,6 +1174,14 @@ application, then in the command palette of VS Code, enter "Remote-Containers:
 Open Folder in Container", and hit :kbd:`Enter`, and choose the directory
 ``$SAGE_ROOT`` of your local Sage repository.
 
+VS Code then prompts you to choose a dev container configuration. 
+For example, choose "Ubuntu jammy" `.devcontainer/portability-ubuntu-jammy-standard/devcontainer.json
+<https://github.com/sagemath/sage/tree/develop/.devcontainer/portability-ubuntu-jammy-standard/devcontainer.json>`_,
+which uses the Docker image based on ``ubuntu-jammy-standard``, the most recent
+development version of Sage (``dev`` tag), and a full installation of
+the Sage distribution (``with-targets``). Other dev container configurations
+are described below.
+
 Once VS Code starts configuring the dev container, by clicking on "show log",
 you can see what it does:
 
@@ -1225,8 +1217,7 @@ in a terminal, `open a new terminal in VS Code
    ``configure`` script.
 
 You can edit a copy of the configuration file to change to a different platform, another
-version, or build stage.  After editing the configuration file (or changing the
-symlink), run "Remote-Containers: Rebuild Container" from the command
+version, or build stage.  After editing the configuration file, run "Remote-Containers: Rebuild Container" from the command
 palette. See the `VS Code devcontainer.json reference
 <https://code.visualstudio.com/docs/remote/devcontainerjson-reference>`_
 and the `GitHub introduction to dev containers
@@ -1248,8 +1239,7 @@ installation of SageMath in this container by building from the current source t
   project <https://hub.docker.com/r/computop/sage/>`_, providing
   SnapPy, Regina, PHCPack, etc.
 
-If you want to use one of these ``devcontainer.json`` files, symlink (or copy)
-it and start VS Code as explained above. After VS Code finished configuring the
+After VS Code finished configuring the
 dev container, to use Sage in a terminal, `open a new terminal in VS Code
 <https://code.visualstudio.com/docs/terminal/basics>`_, type ``./sage`` and hit
 :kbd:`Enter`.
@@ -1284,8 +1274,7 @@ work without change) or to adapt them to your needs.
   project <https://hub.docker.com/r/computop/sage/>`_, providing
   SnapPy, Regina, PHCPack, etc.
 
-If you want to use one of these ``devcontainer.json`` files, symlink (or copy)
-it and start VS Code as explained above. After VS Code finished configuring the
+After VS Code finished configuring the
 dev container, to use Sage in a terminal, `open a new terminal in VS Code
 <https://code.visualstudio.com/docs/terminal/basics>`_, type ``sage`` and hit
 :kbd:`Enter`. (Do not use ``./sage``; this will not work because the source

src/sage/combinat/designs/difference_family.py

@@ -1892,7 +1892,7 @@ def get_fixed_relative_difference_set(rel_diff_set, as_elements=False):
 
 def is_fixed_relative_difference_set(R, q):
     r"""Check if the relative difference set `R` is fixed by `q`.
-    
+
     A relative difference set  `R` is fixed by `q` if  `\{qd | d \in R\}= R` (see Section 3 of [Spe1975]_).
 
     INPUT:

src/sage/combinat/matrices/hadamard_matrix.py

@@ -90,6 +90,13 @@ def normalise_hadamard(H, skew=False):
         sage: H = normalise_hadamard(skew_hadamard_matrix(20, skew_normalize=False), skew=True)
         sage: is_hadamard_matrix(H, skew=True, normalized=True)
         True
+
+    If ``skew`` is True but the Hadamard matrix is not skew, the matrix returned
+    will not be normalized::
+
+        sage: H = normalise_hadamard(hadamard_matrix(92), skew=True)
+        sage: is_hadamard_matrix(H, normalized=True)
+        False
     """
 
     if skew:
@@ -2274,7 +2281,7 @@ def skew_hadamard_matrix_spence_construction(n, check=True):
     r"""
     Construct skew Hadamard matrix of order `n` using Spence constrution.
 
-    This function will construct skew Hadamrd matrix of order `n=2(q+1)` where `q` is
+    This function will construct skew Hadamard matrix of order `n=2(q+1)` where `q` is
     a prime power with `q = 5` (mod 8). The construction is taken from [Spe1977]_, and the
     relative difference sets are constructed using :func:`sage.combinat.designs.difference_family.relative_difference_set_from_homomorphism`.
 
@@ -2364,6 +2371,7 @@ def GS_skew_hadamard_smallcases(n, existence=False, check=True):
     Namely, it needs 4 circulant matrices with extra properties, as described in
     :func:`sage.combinat.matrices.hadamard_matrix.williamson_goethals_seidel_skew_hadamard_matrix`
     Matrices are taken from:
+
     * `n=36, 52`: [GS70s]_
     * `n=92`: [Wall71]_
     * `n=188`: [Djo2008a]_
@@ -2607,7 +2615,7 @@ def skew_hadamard_matrix_from_good_matrices(a, b, c, d, check=True):
 
     - ``c`` -- (1,-1) list specifying the 1st row of `D`.
 
-    - ``check`` -- boolean: if True (default), check the the matrix is an Hadamard matrix before returning it.
+    - ``check`` -- boolean: if True (default), check that the matrix is a skew Hadamard matrix before returning it.
 
     EXAMPLES::
 

src/sage/schemes/toric/sheaf/klyachko.py

@@ -26,7 +26,7 @@
     (0, 0, 18, 16, 1)
     sage: Gtilde = G_sum.random_deformation()
     sage: V = Gtilde.wedge(2) * K                     # long time
-    sage: V.cohomology(dim=True, weight=(0,0,0,0))    # long time
+    sage: V.cohomology(dim=True, weight=(0,0,0,0))    # long time  # random failure (see #32773)
     (0, 0, 3, 0, 0)
 
 REFERENCES:
@@ -948,7 +948,7 @@ def random_deformation(self, epsilon=None):
            sage: V.cohomology(dim=True, weight=(0,))
            (1, 0)
            sage: Vtilde = V.random_deformation()
-           sage: Vtilde.cohomology(dim=True, weight=(0,))
+           sage: Vtilde.cohomology(dim=True, weight=(0,))  # random failure (see #32773)
            (1, 0)
         """
         filt = self._filt.random_deformation(epsilon)

tox.ini

@@ -272,7 +272,6 @@ setenv =
     fedora-31:        BASE_TAG=31
     fedora-32:        BASE_TAG=32
     fedora-33:        BASE_TAG=33
-    fedora-33:                                 IGNORE_MISSING_SYSTEM_PACKAGES=no
     fedora-34:        BASE_TAG=34
     fedora-34:                                 IGNORE_MISSING_SYSTEM_PACKAGES=no
     fedora-35:        BASE_TAG=35