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Merge branch 'master' into dependabot/github_actions/pypa/gh-action-pypi-publish-1.12.4
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‎.github/workflows/ci.yml

Lines changed: 37 additions & 118 deletions
Original file line numberDiff line numberDiff line change
@@ -13,96 +13,23 @@ jobs:
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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-20.04", "ubuntu-latest", "macos-latest"]
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compiler: [gcc-7, gcc-9, clang]
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python-version: ["3.9", "3.12"]
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numpy-version: ["1.20", "2.0.1"]
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include:
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- numpy-version: "1.23"
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compiler: gcc-10
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python-version: "3.10"
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os: ubuntu-latest
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- numpy-version: "1.23"
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compiler: gcc-11
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python-version: "3.10"
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os: ubuntu-latest
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- numpy-version: "1.23"
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compiler: gcc-10
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python-version: "3.10"
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os: ubuntu-latest
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- numpy-version: "1.23"
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compiler: gcc-11
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python-version: "3.10"
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os: ubuntu-latest
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- numpy-version: "1.23"
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compiler: gcc-10
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python-version: "3.11"
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os: ubuntu-latest
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- numpy-version: "1.23"
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compiler: gcc-11
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python-version: "3.11"
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os: ubuntu-latest
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- numpy-version: "1.23"
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compiler: gcc-12
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python-version: "3.11"
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os: ubuntu-latest
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- numpy-version: "1.23"
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compiler: gcc-10
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python-version: "3.11"
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os: ubuntu-latest
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- numpy-version: "1.23"
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compiler: gcc-11
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python-version: "3.11"
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os: ubuntu-latest
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- numpy-version: "1.23"
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compiler: gcc-12
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python-version: "3.11"
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os: ubuntu-latest
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exclude:
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# Only run with 'clang' on OSX
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- os: "macos-latest"
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compiler: gcc-7
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- os: "macos-latest"
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compiler: gcc-9
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# Don't use 'clang' on linux
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- os: "ubuntu-20.04"
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- os: ubuntu-24.04
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compiler: gcc
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python-version: 3.9
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numpy-version: 1
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- os: ubuntu-24.04
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compiler: gcc
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python-version: 3.13
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numpy-version: 2
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- os: macos-14
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compiler: clang
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- os: "ubuntu-latest"
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python-version: 3.9
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numpy-version: 1
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- os: macos-14
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compiler: clang
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# only gcc-10 on latest
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- os: "ubuntu-latest"
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compiler: gcc-9
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- os: "ubuntu-latest"
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compiler: gcc-7
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# Only use latest numpy on ubuntu-latest
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- os: "ubuntu-latest"
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numpy-version: 1.20
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# python3.10 only on ubuntu-latest
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# - os: "ubuntu-20.04"
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# python-version: "3.10"
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# - os: "macos-latest"
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# python-version: "3.10"
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- python-version: "3.9"
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numpy-version: "2.0.1"
103-
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- python-version: "3.12"
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numpy-version: "1.20"
31+
python-version: 3.13
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numpy-version: 2
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env:
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CC: ${{ matrix.compiler }}
@@ -116,32 +43,16 @@ jobs:
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uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
46+
miniforge-version: latest
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conda-remove-defaults: true
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auto-activate-base: false
120-
miniconda-version: 'latest'
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python-version: ${{ matrix.python-version }}
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# This was needed on 18.04 but not on 20.04
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# - name: Install binutils on linux
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# shell: bash -l {0}
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# if: matrix.os == 'ubuntu-18.04'
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# run: |
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# sudo apt-get update
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# sudo apt-get install binutils
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- name: Install gcc-7 on ubuntu-20.04
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shell: bash -l {0}
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if: matrix.os == 'ubuntu-20.04'
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run: |
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sudo add-apt-repository ppa:ubuntu-toolchain-r/test
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sudo apt-get update
137-
sudo apt-get install gcc-7
49+
activate-environment: ""
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13951
- name: Install dependencies
14052
shell: bash -l {0}
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run: |
142-
conda create -q --yes -n test python=${{ matrix.python-version }} nomkl
54+
conda create -n test python=${{ matrix.python-version }} numpy=${{ matrix.numpy-version }} nomkl gsl
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conda activate test
144-
conda install -q --yes -c conda-forge numpy=${{ matrix.numpy-version }} gsl
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- name: Display PATH, compiler, python
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shell: bash -l {0}
@@ -156,48 +67,56 @@ jobs:
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echo `${{ matrix.compiler }} -dM -E - -march=native`
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15869
- name: lscpu on Linux
159-
if: matrix.os != 'macos-latest'
70+
if: matrix.os != 'macos-14'
16071
run: |
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lscpu
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- name: sysctl machdep.cpu on OSX
164-
if: matrix.os == 'macos-latest'
75+
if: matrix.os == 'macos-14'
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run: |
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sysctl machdep.cpu
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# - name: Add linker flag to OSX + gcc
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# shell: bash -l {0}
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# if: matrix.os == 'osx-latest' && startswith(matrix.compiler, 'gcc')
171-
# run: export CLINK = '-lgomp'
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- name: compile
17480
shell: bash -l {0}
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run: make -r CC=${{ matrix.compiler }}
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run: |
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conda activate test
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make -r CC=${{ matrix.compiler }}
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- name: install
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shell: bash -l {0}
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run: make install CC=${{ matrix.compiler }}
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run: |
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conda activate test
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make install CC=${{ matrix.compiler }}
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- name: compile and install python extensions
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shell: bash -l {0}
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run: |
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conda activate test
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echo "CC = " $CC
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export CC=${{ matrix.compiler }}
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python -m pip install -e .
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- name: tests
189100
shell: bash -l {0}
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run: make tests CC=${{ matrix.compiler }}
101+
run: |
102+
conda activate test
103+
make tests CC=${{ matrix.compiler }}
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- name: doctests
193106
shell: bash -l {0}
194-
if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10' && matrix.numpy-version == '1.16'
107+
if: matrix.os == 'ubuntu-24.04' && matrix.python-version == '3.13' && matrix.numpy-version == '2'
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run: |
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conda activate test
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python -m pip install 'sphinx>=1.8'
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make -C docs doctest
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- name: Python tests
200114
shell: bash -l {0}
201115
run: |
116+
conda activate test
117+
if [ "${{ matrix.os }}" = "macos-14" ]; then
118+
# We currently don't build with OpenMP on MacOS in CI
119+
export CORRFUNC_PYTEST_MAX_THREADS=1
120+
fi
202121
python -m pip install pytest
203122
python -m pytest -v

‎Corrfunc/tests/common.py

Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -54,6 +54,10 @@ def maxthreads():
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maxthreads = len(os.sched_getaffinity(0))
5555
except AttributeError:
5656
maxthreads = multiprocessing.cpu_count() or 1
57+
58+
environ_max = os.environ.get('CORRFUNC_PYTEST_MAX_THREADS')
59+
if environ_max:
60+
maxthreads = min(int(environ_max), maxthreads)
5761

5862
return maxthreads
5963

@@ -63,16 +67,15 @@ def generate_isa_and_nthreads_combos(extra_isa=None):
6367
mx = maxthreads()
6468

6569
# the ISA sweep will use maxthreads
66-
# and then with the fastest ISA, we will test single-threaded,
67-
# plus "oversubscribed", where we use more threads than cores
68-
all_nthreads = [1,mx+1]
70+
# and then with the fastest ISA, we will test single-threaded
71+
extra_nthreads = [1] if mx > 1 else []
6972

7073
combos = []
7174
all_isa = ['fallback','sse42','avx','avx512f']
7275
if extra_isa:
7376
all_isa += extra_isa
7477
combos += [(isa,mx) for isa in all_isa]
75-
combos += [('fastest',n) for n in all_nthreads]
78+
combos += [('fastest',n) for n in extra_nthreads]
7679

7780
return combos
7881

‎Corrfunc/utils.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -456,7 +456,7 @@ def fix_ra_dec(ra, dec):
456456
if max(dec) > 90.0:
457457
print("Warning: found DEC values more than 90.0; wrapping into "
458458
"[-90.0, 90.0] range")
459-
dec += 90.0
459+
dec -= 90.0
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461461
return ra.astype(input_dtype), dec.astype(input_dtype)
462462

‎docs/source/conf.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -83,7 +83,7 @@
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#
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# This is also used if you do content translation via gettext catalogs.
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# Usually you set "language" from the command line for these cases.
86-
language = None
86+
language = 'en'
8787

8888
# There are two options for replacing |today|: either, you set today to some
8989
# non-false value, then it is used:
@@ -375,6 +375,6 @@
375375

376376

377377
# Example configuration for intersphinx: refer to the Python standard library.
378-
intersphinx_mapping = {'https://docs.python.org/': None}
378+
intersphinx_mapping = {'python': ('https://docs.python.org/', None)}
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380380
del sys.path[0]

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