Merge branch 'master' into dependabot/github_actions/pypa/gh-action-p…

…ypi-publish-1.12.4

.github/workflows/ci.yml

@@ -13,96 +13,23 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-20.04", "ubuntu-latest", "macos-latest"]
-        compiler: [gcc-7, gcc-9, clang]
-        python-version: ["3.9", "3.12"]
-        numpy-version: ["1.20", "2.0.1"]
-
         include:
-          - numpy-version: "1.23"
-            compiler: gcc-10
-            python-version: "3.10"
-            os: ubuntu-latest
-
-          - numpy-version: "1.23"
-            compiler: gcc-11
-            python-version: "3.10"
-            os: ubuntu-latest
-
-          - numpy-version: "1.23"
-            compiler: gcc-10
-            python-version: "3.10"
-            os: ubuntu-latest
-
-          - numpy-version: "1.23"
-            compiler: gcc-11
-            python-version: "3.10"
-            os: ubuntu-latest
-
-          - numpy-version: "1.23"
-            compiler: gcc-10
-            python-version: "3.11"
-            os: ubuntu-latest
-
-          - numpy-version: "1.23"
-            compiler: gcc-11
-            python-version: "3.11"
-            os: ubuntu-latest
-
-          - numpy-version: "1.23"
-            compiler: gcc-12
-            python-version: "3.11"
-            os: ubuntu-latest
-
-          - numpy-version: "1.23"
-            compiler: gcc-10
-            python-version: "3.11"
-            os: ubuntu-latest
-
-          - numpy-version: "1.23"
-            compiler: gcc-11
-            python-version: "3.11"
-            os: ubuntu-latest
-
-          - numpy-version: "1.23"
-            compiler: gcc-12
-            python-version: "3.11"
-            os: ubuntu-latest
-
-        exclude:
-          # Only run with 'clang' on OSX
-          - os: "macos-latest"
-            compiler: gcc-7
-          - os: "macos-latest"
-            compiler: gcc-9
-
-          # Don't use 'clang' on linux
-          - os: "ubuntu-20.04"
+          - os: ubuntu-24.04
+            compiler: gcc
+            python-version: 3.9
+            numpy-version: 1
+          - os: ubuntu-24.04
+            compiler: gcc
+            python-version: 3.13
+            numpy-version: 2
+          - os: macos-14
             compiler: clang
-          - os: "ubuntu-latest"
+            python-version: 3.9
+            numpy-version: 1
+          - os: macos-14
             compiler: clang
-
-          # only gcc-10 on latest
-          - os: "ubuntu-latest"
-            compiler: gcc-9
-          - os: "ubuntu-latest"
-            compiler: gcc-7
-
-          # Only use latest numpy on ubuntu-latest  
-          - os: "ubuntu-latest"
-            numpy-version: 1.20
-
-          # python3.10 only on ubuntu-latest
-          # - os: "ubuntu-20.04"
-          #   python-version: "3.10"
-          # - os: "macos-latest"
-          #   python-version: "3.10"
-
-          - python-version: "3.9"
-            numpy-version: "2.0.1"
-
-          - python-version: "3.12"
-            numpy-version: "1.20"
+            python-version: 3.13
+            numpy-version: 2
 
     env:
       CC: ${{ matrix.compiler }}
@@ -116,32 +43,16 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
+          miniforge-version: latest
+          conda-remove-defaults: true
           auto-activate-base: false
-          miniconda-version: 'latest'
-          python-version: ${{ matrix.python-version }}
-
-      # This was needed on 18.04 but not on 20.04
-      # - name: Install binutils on linux
-      #   shell: bash -l {0}
-      #   if: matrix.os == 'ubuntu-18.04'
-      #   run: |
-      #     sudo apt-get update
-      #     sudo apt-get install binutils
-
-      - name: Install gcc-7 on ubuntu-20.04
-        shell: bash -l {0}
-        if: matrix.os == 'ubuntu-20.04'
-        run: |
-          sudo add-apt-repository ppa:ubuntu-toolchain-r/test
-          sudo apt-get update
-          sudo apt-get install gcc-7
+          activate-environment: ""
 
       - name: Install dependencies
         shell: bash -l {0}
         run: |
-          conda create -q --yes -n test python=${{ matrix.python-version }} nomkl
+          conda create -n test python=${{ matrix.python-version }} numpy=${{ matrix.numpy-version }} nomkl gsl
           conda activate test
-          conda install -q --yes -c conda-forge numpy=${{ matrix.numpy-version }} gsl
 
       - name: Display PATH, compiler, python
         shell: bash -l {0}
@@ -156,48 +67,56 @@ jobs:
           echo `${{ matrix.compiler }} -dM -E - -march=native`
 
       - name: lscpu on Linux
-        if: matrix.os != 'macos-latest'
+        if: matrix.os != 'macos-14'
         run: |
           lscpu
 
       - name: sysctl machdep.cpu on OSX
-        if: matrix.os == 'macos-latest'
+        if: matrix.os == 'macos-14'
         run: |
           sysctl machdep.cpu
 
-#      - name: Add linker flag to OSX + gcc
-#        shell: bash -l {0}
-#        if: matrix.os == 'osx-latest' && startswith(matrix.compiler, 'gcc')
-#        run: export CLINK = '-lgomp'
-
       - name: compile
         shell: bash -l {0}
-        run: make -r CC=${{ matrix.compiler }}
+        run: |
+          conda activate test
+          make -r CC=${{ matrix.compiler }}
 
       - name: install
         shell: bash -l {0}
-        run: make install CC=${{ matrix.compiler }}
+        run: |
+          conda activate test
+          make install CC=${{ matrix.compiler }}
 
       - name: compile and install python extensions
         shell: bash -l {0}
         run: |
+          conda activate test
           echo "CC = " $CC
           export CC=${{ matrix.compiler }}
           python -m pip install -e .
 
       - name: tests
         shell: bash -l {0}
-        run: make tests CC=${{ matrix.compiler }}
+        run: |
+          conda activate test
+          make tests CC=${{ matrix.compiler }}
 
       - name: doctests
         shell: bash -l {0}
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10' && matrix.numpy-version == '1.16'
+        if: matrix.os == 'ubuntu-24.04' && matrix.python-version == '3.13' && matrix.numpy-version == '2'
         run: |
+          conda activate test
           python -m pip install 'sphinx>=1.8'
           make -C docs doctest
 
       - name: Python tests
         shell: bash -l {0}
         run: |
+          conda activate test
+          if [ "${{ matrix.os }}" = "macos-14" ]; then
+            # We currently don't build with OpenMP on MacOS in CI
+            export CORRFUNC_PYTEST_MAX_THREADS=1
+          fi
           python -m pip install pytest
           python -m pytest -v

Corrfunc/tests/common.py

@@ -54,6 +54,10 @@ def maxthreads():
         maxthreads = len(os.sched_getaffinity(0))
     except AttributeError:
         maxthreads = multiprocessing.cpu_count() or 1
+
+    environ_max = os.environ.get('CORRFUNC_PYTEST_MAX_THREADS')
+    if environ_max:
+        maxthreads = min(int(environ_max), maxthreads)
 
     return maxthreads
 
@@ -63,16 +67,15 @@ def generate_isa_and_nthreads_combos(extra_isa=None):
     mx = maxthreads()
 
     # the ISA sweep will use maxthreads
-    # and then with the fastest ISA, we will test single-threaded,
-    # plus "oversubscribed", where we use more threads than cores
-    all_nthreads = [1,mx+1]
+    # and then with the fastest ISA, we will test single-threaded
+    extra_nthreads = [1] if mx > 1 else []
 
     combos = []
     all_isa = ['fallback','sse42','avx','avx512f']
     if extra_isa:
         all_isa += extra_isa
     combos += [(isa,mx) for isa in all_isa]
-    combos += [('fastest',n) for n in all_nthreads]
+    combos += [('fastest',n) for n in extra_nthreads]
 
     return combos
 

Corrfunc/utils.py

@@ -456,7 +456,7 @@ def fix_ra_dec(ra, dec):
     if max(dec) > 90.0:
         print("Warning: found DEC values more than 90.0; wrapping into "
               "[-90.0, 90.0] range")
-        dec += 90.0
+        dec -= 90.0
 
     return ra.astype(input_dtype), dec.astype(input_dtype)
 

docs/source/conf.py

@@ -83,7 +83,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -375,6 +375,6 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'python': ('https://docs.python.org/', None)}
 
 del sys.path[0]