add support of numpy2.0

Add support of numpy2.0
cds-astro · Oct 17, 2024 · 744a8fc · 744a8fc
2 parents b253f10 + c8f6fc4
commit 744a8fc
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Showing 9 changed files with 68 additions and 45 deletions.
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -26,7 +26,7 @@ jobs:
         MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN_FXP }}
        run: |
          source $HOME/.cargo/env
-         for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
+         for PYBIN in /opt/python/cp3{8,9,10,11,12,13}-*/bin; do
            "${PYBIN}/pip" install --upgrade pip
            "${PYBIN}/pip" install maturin
            "${PYBIN}/maturin" publish -i "${PYBIN}/python" --skip-existing --compatibility manylinux_2_28
@@ -52,7 +52,7 @@ jobs:
         MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN_FXP }}
        run: |
          source $HOME/.cargo/env
-         for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
+         for PYBIN in /opt/python/cp3{8,9,10,11,12,13}-*/bin; do
            "${PYBIN}/pip" install --upgrade pip
            "${PYBIN}/pip" install maturin
            "${PYBIN}/maturin" publish -i "${PYBIN}/python" --skip-existing --compatibility manylinux2014
@@ -64,7 +64,7 @@ jobs:
     runs-on: ubuntu-latest
     # CentOS 7 32 bits Docker Hub image that 'build-linux-wheels' executes in.
     # See https://github.com/pypa/manylinux for this particular container:
-    # * CPython 3.7, 3.8, 3.9, 3.10, 3.11, and 3.12 installed in /opt/python/<python tag>-<abi tag>
+    # * CPython 3.7, 3.8, 3.9, 3.10, 3.11, 3.12, 13 installed in /opt/python/<python tag>-<abi tag>
     env:
       MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN_FXP }}
       img: quay.io/pypa/manylinux2014_i686
@@ -81,7 +81,7 @@ jobs:
          ${{ env.img }} \
          bash -exc 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y && \
            source $HOME/.cargo/env && \
-           for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
+           for PYBIN in /opt/python/cp3{8,9,10,11,12,13}-*/bin; do
              echo "Loop on PYBIN: $PYBIN"
              "${PYBIN}/pip" install --upgrade pip
              "${PYBIN}/pip" install maturin
@@ -108,7 +108,7 @@ jobs:
          ${{ env.img }} \
          bash -exc 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- --default-host aarch64-unknown-linux-gnu -y && \
            source $HOME/.cargo/env && \
-           for PYBIN in /opt/python/cp3{8,9,10,11,12}-*/bin; do
+           for PYBIN in /opt/python/cp3{8,9,10,11,12,13}-*/bin; do
              echo "Loop on PYBIN: $PYBIN"
              "${PYBIN}/pip" install maturin
              "${PYBIN}/maturin" -V
@@ -158,7 +158,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
      # Checkout the project
      - uses: actions/checkout@v4

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [unreleased]
 
+## [0.17.0]
+
 ### Added
 
 * Add support of `regions.Regions` [#163]

diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "MOCPy"
-version = "0.16.2"
+version = "0.17.0"
 authors = [
   "Matthieu Baumann <matthieu.baumann@astro.unistra.fr>",
   "Thomas Boch <thomas.boch@astro.unistra.fr>",
@@ -28,24 +28,24 @@ bench = true
 crate-type = ["cdylib"]
 
 [dependencies]
-# moc = { version = "0.15", features = ["storage"] }
-moc = { git = 'https://github.com/cds-astro/cds-moc-rust', rev = '361eb278fe782bfc053433495c33e3f16e20cdbd', features = ["storage"] }
-healpix = { package = "cdshealpix", version = "0.6" }
+moc = { version = "0.17", features = ["storage"] }
+#moc = { git = 'https://github.com/cds-astro/cds-moc-rust', rev = '361eb278fe782bfc053433495c33e3f16e20cdbd', features = ["storage"] }
+healpix = { package = "cdshealpix", version = "0.7" }
 # healpix = { package = "cdshealpix", git = 'https://github.com/cds-astro/cds-healpix-rust', branch = 'master' }
 rayon = "1.10"
 num_threads = "0.1"
 
 [dependencies.numpy]
-version = "0.21"
+version = "0.22"
 
 [dependencies.ndarray]
-version = "0.15"
+version = "0.16"
 default-features = false # do not include the default features, and optionally
                          # cherry-pick individual features
 features = ["rayon"]
 
 [dependencies.pyo3]
-version = "0.21"
+version = "0.22"
 features = ["extension-module"]
 
 [profile.release]

diff --git a/codemeta.json b/codemeta.json
@@ -9,8 +9,8 @@
     "dateModified": "2023-12-04",
     "issueTracker": "https://github.com/cds-astro/mocpy/issues",
     "name": "MOCpy",
-    "version": "0.16.2",
-    "softwareVersion": "0.16.2",
+    "version": "0.17.0",
+    "softwareVersion": "0.17.0",
     "description": "Python library to easily create and manipulate MOCs (Multi-Order Coverage maps)",
     "applicationCategory": ["Astronomy", "Science"],
     "funding": "ESCAPE 824064, ASTERICS 653477",

diff --git a/pyproject.toml b/pyproject.toml
@@ -8,7 +8,7 @@ requires-python = ">=3.8"
 dependencies = [
     "astropy<5.3; python_version == '3.8'",
     "astropy; python_version > '3.8'",
-    "numpy<2.0",
+    "numpy",
     "matplotlib",     # Used in fill and border
     "cdshealpix>=0.6.4",     # Used in fill and border
     "networkx>=2.5",         # Used in get_boundaries
@@ -18,8 +18,16 @@ classifiers = [
     "Programming Language :: Python",
     "Programming Language :: Rust",
     "License :: OSI Approved :: BSD License",
-    "Topic :: Scientific/Engineering :: Astronomy"
+    "Topic :: Scientific/Engineering :: Astronomy",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Education",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
+keywords=["astronomy", "astrophysics", "HEALPix"]
 
 [project.optional-dependencies]
 # optional to load FITS from URLs
@@ -29,18 +37,17 @@ astropy_regions = ["regions"]
 # for the documentation
 docs = [
     "astropy-sphinx-theme",
-    "astropy_healpix",
     "nbsphinx",
     "numpydoc",
     "sphinx-astropy",
     "sphinx-collections",
     "sphinx-copybutton",
     "sphinx-gallery",
-    "sphinxcontrib-bibtex"
+    "sphinxcontrib-bibtex",
+    "ipython" # for syntaxic coloration in docs
 ]
 # for developpement
 dev = [
-    "astropy_healpix",
     "pre-commit >= 2.20",
     "pytest > 6.0",
     "pytest-mock",
@@ -58,7 +65,10 @@ notebooks = [
 ]
 
 [project.urls]
-repository = "https://github.com/cds-astro/mocpy"
+Documentation = "https://cds-astro.github.io/mocpy/"
+Repository = "https://github.com/cds-astro/mocpy"
+Issues = "https://github.com/cds-astro/mocpy/issues"
+Changelog = "https://github.com/cds-astro/mocpy/blob/master/CHANGELOG.md"
 
 # Build a mocpy-x.x.x.tar.gz containing sources (from maturin).
 [build-system]

diff --git a/python/mocpy/fmoc/fmoc.py b/python/mocpy/fmoc/fmoc.py
@@ -44,7 +44,7 @@ def max_order(self):
         --------
         >>> from mocpy import FrequencyMOC
         >>> fmoc = FrequencyMOC.from_json({8: [12, 14, 16], 22: [120, 121, 122]})
-        >>> fmoc.max_order
+        >>> print(fmoc.max_order)
         22
         """
         depth = mocpy.get_fmoc_depth(self.store_index)

diff --git a/python/mocpy/moc/moc.py b/python/mocpy/moc/moc.py
@@ -2346,7 +2346,7 @@ def wcs(
         >>> import matplotlib.pyplot as plt
         >>> moc = MOC.from_str("2/2-25 28 29 4/0 6/")
         >>> fig = plt.figure()
-        >>> moc.wcs(fig) # DOCTEST: +IGNORE_RESULT
+        >>> moc.wcs(fig) # doctest: +SKIP
         WCS Keywords
         <BLANKLINE>
         Number of WCS axes: 2

diff --git a/python/mocpy/version.py b/python/mocpy/version.py
@@ -1 +1 @@
-__version__ = "0.16.2"
+__version__ = "0.17.0"
diff --git a/src/lib.rs b/src/lib.rs
@@ -1,12 +1,13 @@
 use std::{f64::consts::FRAC_PI_3, ops::Range};
 
-use ndarray::Array;
 #[cfg(not(target_arch = "wasm32"))]
 use num_threads::num_threads;
 use numpy::{
   IntoPyArray, Ix2, Ix3, PyArray1, PyArray2, PyArray3, PyArrayDyn, PyArrayMethods,
   PyReadonlyArray1, PyReadonlyArray2, PyReadonlyArrayDyn, PyUntypedArrayMethods,
 };
+use numpy::ndarray::Array;
+
 use pyo3::{
   exceptions::{PyIOError, PyValueError},
   prelude::{pymodule, Bound, PyModule, PyResult, Python},
@@ -172,6 +173,7 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
   /// * `delta_depth`: precision parameter
   /// * `n_threads`: number of threads to use (max number of threads if `n_threads=None`.
   #[pyfn(m)]
+  #[pyo3(signature = (lon_deg, lat_deg, radius_deg, depth, delta_depth, n_threads=None))]
   fn from_same_cones(
     lon_deg: PyReadonlyArrayDyn<f64>,
     lat_deg: PyReadonlyArrayDyn<f64>,
@@ -248,6 +250,7 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
   /// * `delta_depth`: precision parameter
   /// * `n_threads`: number of threads to use (max number of threads if `n_threads=None`.
   #[pyfn(m)]
+  #[pyo3(signature = (lon_deg, lat_deg, radius_deg, depth, delta_depth, n_threads=None))]
   fn from_cones(
     lon_deg: PyReadonlyArrayDyn<f64>,
     lat_deg: PyReadonlyArrayDyn<f64>,
@@ -328,6 +331,7 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
   /// * `delta_depth`: precision parameter
   /// * `n_threads`: number of threads to use (max number of threads if `n_threads=None`.
   #[pyfn(m)]
+  #[pyo3(signature = (lon_deg, lat_deg, radius_deg, depth, delta_depth, n_threads=None))]
   fn from_small_cones(
     lon_deg: PyReadonlyArrayDyn<f64>,
     lat_deg: PyReadonlyArrayDyn<f64>,
@@ -403,6 +407,7 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
   /// * `delta_depth`: precision parameter
   /// * `n_threads`: number of threads to use (max number of threads if `n_threads=None`.
   #[pyfn(m)]
+  #[pyo3(signature = (lon_deg, lat_deg, radius_deg, depth, delta_depth, n_threads=None))]
   fn from_large_cones(
     lon_deg: PyReadonlyArrayDyn<f64>,
     lat_deg: PyReadonlyArrayDyn<f64>,
@@ -507,6 +512,7 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
   /// # Output
   /// - The MOC indices in the storage
   #[pyfn(m)]
+  #[pyo3(signature = (lon_deg, lat_deg, a, b, angle, depth, n_threads=None))]
   pub fn from_same_boxes(
     lon_deg: PyReadonlyArrayDyn<f64>,
     lat_deg: PyReadonlyArrayDyn<f64>,
@@ -591,6 +597,7 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
   /// # Output
   /// - The MOC indices in the storage
   #[pyfn(m)]
+  #[pyo3(signature = (lon_deg, lat_deg, a, b, pa, depth, n_threads=None))]
   pub fn from_boxes(
     lon_deg: PyReadonlyArrayDyn<f64>,
     lat_deg: PyReadonlyArrayDyn<f64>,
@@ -685,6 +692,7 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
   /// # Output
   /// - The MOC index in the storage
   #[pyfn(m)]
+  #[pyo3(signature = (lon_deg, lat_deg, a, b, pa, depth, n_threads=None))]
   pub fn from_small_boxes(
     lon_deg: PyReadonlyArrayDyn<f64>,
     lat_deg: PyReadonlyArrayDyn<f64>,
@@ -773,6 +781,7 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
   /// # Output
   /// - The MOC index in the storage
   #[pyfn(m)]
+  #[pyo3(signature = (lon_deg, lat_deg, a, b, pa, depth, n_threads=None))]
   pub fn from_large_boxes(
     lon_deg: PyReadonlyArrayDyn<f64>,
     lat_deg: PyReadonlyArrayDyn<f64>,
@@ -970,6 +979,7 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
   /// * `depth`: MOC depth
   /// * `n_threads`: number of threads to use (max number of threads if `n_threads=None`.
   #[pyfn(m)]
+  #[pyo3(signature = (lon_lat_deg, complement, depth, n_threads=None))]
   pub fn from_polygons(
     lon_lat_deg: Vec<PyReadonlyArrayDyn<f64>>,
     complement: bool,
@@ -1129,9 +1139,9 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
     lat: PyReadonlyArrayDyn<f64>,
     d2: u8,
   ) -> PyResult<usize> {
-    let times = times.as_array().to_owned().into_raw_vec();
-    let lon = lon.as_array().to_owned().into_raw_vec();
-    let lat = lat.as_array().to_owned().into_raw_vec();
+    let times = times.to_vec().map_err(PyValueError::new_err)?;
+    let lon = lon.to_vec().map_err(PyValueError::new_err)?;
+    let lat = lat.to_vec().map_err(PyValueError::new_err)?;
 
     U64MocStore::get_global_store()
       .create_from_times_positions_approx(times, lon, lat, d1, d2)
@@ -1167,9 +1177,9 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
     lat: PyReadonlyArrayDyn<f64>,
     d2: u8,
   ) -> PyResult<usize> {
-    let times = times.as_array().to_owned().into_raw_vec();
-    let lon = lon.as_array().to_owned().into_raw_vec();
-    let lat = lat.as_array().to_owned().into_raw_vec();
+    let times = times.to_vec().map_err(PyValueError::new_err)?;
+    let lon = lon.to_vec().map_err(PyValueError::new_err)?;
+    let lat = lat.to_vec().map_err(PyValueError::new_err)?;
 
     U64MocStore::get_global_store()
       .create_from_times_positions(times, lon, lat, d1, d2)
@@ -1214,10 +1224,10 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
     lat: PyReadonlyArrayDyn<f64>,
     d2: u8,
   ) -> PyResult<usize> {
-    let times_min = times_min.as_array().to_owned().into_raw_vec();
-    let times_max = times_max.as_array().to_owned().into_raw_vec();
-    let lon = lon.as_array().to_owned().into_raw_vec();
-    let lat = lat.as_array().to_owned().into_raw_vec();
+    let times_min = times_min.to_vec().map_err(PyValueError::new_err)?;
+    let times_max = times_max.to_vec().map_err(PyValueError::new_err)?;
+    let lon = lon.to_vec().map_err(PyValueError::new_err)?;
+    let lat = lat.to_vec().map_err(PyValueError::new_err)?;
 
     U64MocStore::get_global_store()
       .create_from_time_ranges_positions_approx(times_min, times_max, d1, lon, lat, d2)
@@ -1256,10 +1266,10 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
     lat: PyReadonlyArrayDyn<f64>,
     d2: u8,
   ) -> PyResult<usize> {
-    let times_min = times_min.as_array().to_owned().into_raw_vec();
-    let times_max = times_max.as_array().to_owned().into_raw_vec();
-    let lon = lon.as_array().to_owned().into_raw_vec();
-    let lat = lat.as_array().to_owned().into_raw_vec();
+    let times_min = times_min.to_vec().map_err(PyValueError::new_err)?;
+    let times_max = times_max.to_vec().map_err(PyValueError::new_err)?;
+    let lon = lon.to_vec().map_err(PyValueError::new_err)?;
+    let lat = lat.to_vec().map_err(PyValueError::new_err)?;
 
     U64MocStore::get_global_store()
       .create_from_time_ranges_positions(times_min, times_max, d1, lon, lat, d2)
@@ -1303,14 +1313,14 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
     d1: u8,
     spatial_coverages: PyReadonlyArrayDyn<usize>,
   ) -> PyResult<usize> {
-    let times_min = times_min.as_array().to_owned().into_raw_vec();
-    let times_max = times_max.as_array().to_owned().into_raw_vec();
+    let times_min = times_min.to_vec().map_err(PyValueError::new_err)?;
+    let times_max = times_max.to_vec().map_err(PyValueError::new_err)?;
     if times_min.len() != times_max.len() {
       return Err(PyValueError::new_err(
         "`times_min` and `times_max` do not have the same size.",
       ));
     }
-    let spatial_coverage_indices = spatial_coverages.as_array().to_owned().into_raw_vec();
+    let spatial_coverage_indices = spatial_coverages.to_vec().map_err(PyValueError::new_err)?;
     if times_min.len() != spatial_coverage_indices.len() {
       return Err(PyValueError::new_err(
         "`times` and `spatial indices` do not have the same size.",
@@ -1357,14 +1367,14 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
     d1: u8,
     spatial_coverages: PyReadonlyArrayDyn<usize>,
   ) -> PyResult<usize> {
-    let times_min = times_min.as_array().to_owned().into_raw_vec();
-    let times_max = times_max.as_array().to_owned().into_raw_vec();
+    let times_min = times_min.to_vec().map_err(PyValueError::new_err)?;
+    let times_max = times_max.to_vec().map_err(PyValueError::new_err)?;
     if times_min.len() != times_max.len() {
       return Err(PyValueError::new_err(
         "`times_min` and `times_max` do not have the same size.",
       ));
     }
-    let spatial_coverage_indices = spatial_coverages.as_array().to_owned().into_raw_vec();
+    let spatial_coverage_indices = spatial_coverages.to_vec().map_err(PyValueError::new_err)?;
     if times_min.len() != spatial_coverage_indices.len() {
       return Err(PyValueError::new_err(
         "`times` and `spatial indices` do not have the same size.",
@@ -2304,6 +2314,7 @@ fn mocpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
 
   /// Same as `multiorder_probdens_map_sum_in_smoc` but applied on multiple S-MOCs.
   #[pyfn(m)]
+  #[pyo3(signature = (indices, uniq, uniq_mask, probdens, probdens_mask, n_threads=None))]
   fn multi_multiorder_probdens_map_sum_in_smoc<'a>(
     py: Python<'a>,
     indices: PyReadonlyArrayDyn<'a, usize>,