Revert numpy and scipy

pyodide · Jan 13, 2024 · 4993736 · 4993736
1 parent 5a09eef
commit 4993736
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Showing 4 changed files with 41 additions and 77 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -42,52 +42,39 @@ jobs:
 
           which ccache
 
-      # - name: Cache conda
-      #   uses: actions/cache@v2
-      #   with:
-      #     path: ~/conda_pkgs_dir
-      #     key:
-      #       ${{ runner.os }}-conda-${{ env.CONDA_CACHE_NUMBER }}-${{
-      #       hashFiles('environment.yml') }}
-
-      # - name: Setup Mambaforge
-      #   uses: conda-incubator/setup-miniconda@v2
-      #   with:
-      #     miniforge-variant: Mambaforge
-      #     miniforge-version: latest
-      #     activate-environment: pyodide-env
-      #     use-mamba: true
-
-      # - name: Get Date
-      #   id: get-date
-      #   run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
-      #   shell: bash
-
-      # - name: Cache Conda env
-      #   id: conda-cache
-      #   uses: actions/cache@v2
-      #   with:
-      #     path: ${{ env.CONDA }}/envs
-      #     key:
-      #       conda-${{ runner.os }}-${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-${{ env.CONDA_CACHE_NUMBER }}
-
-      # - name: Update environment if cache miss
-      #   run:
-      #     mamba env update -n pyodide-env -f environment.yml
-      #   if: steps.conda-cache.outputs.cache-hit != 'true'
-
-      - uses: actions/setup-python@v5
+      - name: Cache conda
+        uses: actions/cache@v2
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            ${{ runner.os }}-conda-${{ env.CONDA_CACHE_NUMBER }}-${{
+            hashFiles('environment.yml') }}
+
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: '3.11'
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          activate-environment: pyodide-env
+          use-mamba: true
 
-      - uses: actions/setup-node@v4
+      - name: Get Date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache Conda env
+        id: conda-cache
+        uses: actions/cache@v2
         with:
-          node-version: 20
+          path: ${{ env.CONDA }}/envs
+          key:
+            conda-${{ runner.os }}-${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-${{ env.CONDA_CACHE_NUMBER }}
 
-      - name: Install dependencies
-        shell: bash -l {0}
-        run: |
-          sudo apt-get install ccache f2c swig make cmake texinfo autoconf automake libtool wget gfortran build-essential git xxd
+      - name: Update environment if cache miss
+        run:
+          mamba env update -n pyodide-env -f environment.yml
+        if: steps.conda-cache.outputs.cache-hit != 'true'
 
       - name: Install latest pyodide-build and build dependencies
         shell: bash -l {0}

diff --git a/packages/numpy/meta.yaml b/packages/numpy/meta.yaml
@@ -1,24 +1,16 @@
 package:
   name: numpy
-  version: 1.26.1
+  version: 1.25.2
   tag:
     - min-scipy-stack
   top-level:
     - numpy
 source:
-  url: https://files.pythonhosted.org/packages/78/23/f78fd8311e0f710fe1d065d50b92ce0057fe877b8ed7fd41b28ad6865bfc/numpy-1.26.1.tar.gz
-  sha256: c8c6c72d4a9f831f328efb1312642a1cafafaa88981d9ab76368d50d07d93cbe
+  url: https://files.pythonhosted.org/packages/a0/41/8f53eff8e969dd8576ddfb45e7ed315407d27c7518ae49418be8ed532b07/numpy-1.25.2.tar.gz
+  sha256: fd608e19c8d7c55021dffd43bfe5492fab8cc105cc8986f813f8c3c048b38760
 
 build:
-  # numpy uses vendored meson, so we need to pass the cross file manually
-  backend-flags: |
-    setup-args=-Dallow-noblas=true
-    setup-args=--cross-file=${MESON_CROSS_FILE}
-  # numpy creates numpy/distutils/__pycache__ directory during the build.
-  # It breaks our test because there is a .pyc in the directory.
-  post: |
-    cd $WHEELDIR
-    rm -rf numpy/distutils/__pycache__
+  backend-flags: --disable-optimization
   cflags: |
     -Wno-return-type
   cross-build-env: true
@@ -27,9 +19,6 @@ build:
     - numpy/core/include/numpy/_numpyconfig.h
     - numpy/core/lib/libnpymath.a
     - numpy/random/lib/libnpyrandom.a
-requirements:
-  host:
-    - openblas
 about:
   home: https://www.numpy.org
   PyPI: https://pypi.org/project/numpy

diff --git a/packages/scipy/meta.yaml b/packages/scipy/meta.yaml
@@ -27,7 +27,8 @@ source:
     - patches/0004-gemm_-no-const.patch
     - patches/0005-make-int-return-values.patch
     - patches/0006-Rename-_page_trend_test.py-to-prevent-test-unvendori.patch
-    - patches/0008-Remove-test-modules-that-fails-to-build.patch
+    - patches/0007-skip-fortran-fails-to-link.patch
+    - patches/0008-Remove-meson-requirements.patch
     - patches/0009-Fix-fitpack.patch
     - patches/0010-Fix-gees-calls.patch
 
@@ -36,10 +37,7 @@ build:
     -I$(WASM_LIBRARY_DIR)/include
     -Wno-return-type
     -DUNDERSCORE_G77
-    -fvisibility=default
-  cxxflags: |
-    -fexceptions
-    -fvisibility=default
+  cxxflags: -fexceptions
   ldflags: |
     -L$(NUMPY_LIB)/core/lib/
     -L$(NUMPY_LIB)/random/lib/
@@ -51,9 +49,14 @@ build:
   # pyodide-build/pyodide_build/_f2c_fixes.py.
   script: |
     set -x
+    export PKG_CONFIG_LIBDIR=$WASM_PKG_CONFIG_PATH
     export NPY_BLAS_LIBS="-I$WASM_LIBRARY_DIR/include $WASM_LIBRARY_DIR/lib/libopenblas.so"
     export NPY_LAPACK_LIBS="-I$WASM_LIBRARY_DIR/include $WASM_LIBRARY_DIR/lib/libopenblas.so"
 
+    # setup.py has been renamed to _setup.py in scipy 1.11.2 to discourage its
+    # usage but we still need it until we manage to build with meson
+    mv _setup.py setup.py
+
     sed -i 's/recursive //g' scipy/integrate/quadpack/* scipy/interpolate/fitpack/*
     sed -i 's/void DQA/int DQA/g' scipy/integrate/__quadpack.h
 

diff --git a/packages/scipy/test_scipy.py b/packages/scipy/test_scipy.py
@@ -86,18 +86,3 @@ def test_cpp_exceptions(selenium):
 
     with pytest.raises(ValueError):
         lombscargle(x=[1], y=[1, 2], freqs=[1, 2, 3])
-
-
-@pytest.mark.driver_timeout(40)
-@run_in_pyodide(packages=["scipy"])
-def test_logm(selenium_standalone):
-    import numpy as np
-    from numpy import eye, random
-    from scipy.linalg import logm
-
-    random.seed(1234)
-    dtype = np.float64
-    n = 2
-    scale = 1e-4
-    A = (eye(n) + random.rand(n, n) * scale).astype(dtype)
-    logm(A)