Merge pull request #214 from threeML/dev

Dev

.github/workflows/deploy.yml

@@ -73,37 +73,26 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                os: [ubuntu-latest, macos-latest, macos-12]
+                os: [ubuntu-latest, macos-latest, macos-13]
                 python-version: [3.9]
-
+                include:
+                  - environment: ci/environment.yml
+                  - environment:  ci/environment_noxspec.yml
+                    os: macos-latest
         steps:
             - name: Checkout
               uses: actions/checkout@v4
               with:
                   fetch-depth: 0
-            # - name: Set up Python
-            #   uses: actions/setup-python@v5
-            #   with:
-            #       python-version: ${{ matrix.python-version }}
-            # - name: Cache conda
-            #   uses: actions/cache@v4
-            #   env:
-            #     # Increase this value to reset cache if etc/example-environment.yml has not changed
-            #     CACHE_NUMBER: 0
-            #   with:
-            #       path: ~/conda_pkgs_dir
-            #       key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('ci/environment.yml') }}
             - name: Add conda ${{ matrix.python-version }} to system path
               uses: conda-incubator/setup-miniconda@v3
               with:
                   activate-environment: "test_env"
                   auto-activate-base: false
-                  architecture: "x64"
-                  miniforge-variant: Mambaforge
-                  #miniforge-version: latest
+                  miniforge-variant: Miniforge3
                   python-version: ${{ matrix.python-version }}
                   auto-update-conda: true
-                  environment-file: ci/environment.yml
+                  environment-file: ${{ matrix.environment }}
                   use-only-tar-bz2: true
                   channel-priority: true
                   channels: conda-forge, xspecmodels, threeml
@@ -118,7 +107,7 @@ jobs:
                       
                       miniconda_os=Linux
                       compilers="gcc_linux-64 gxx_linux-64 gfortran_linux-64"
-                  else  # osx
+                  else
                       
                       miniconda_os=MacOSX
                       compilers="clang_osx-64 clangxx_osx-64 gfortran_osx-64"
@@ -155,13 +144,15 @@ jobs:
 
                   #conda install --use-local astromodels
                   conda install -c ${CONDA}/envs/test_env/conda-bld/ astromodels
-            - name: Test conda build
+            - name: Test import xspec
+              if: matrix.os != 'macos-latest'
               shell: bash -l {0}
               run: |
                   cd astromodels/tests
-                  echo "======>  importing XSPEC..."
                   python -c "import astromodels.xspec"
-                  python -m pytest -vv --cov=astromodels --cov-report=xml
+            - name: Test astromodels
+              shell: bash -l {0}
+              run: python -m pytest -vv --cov=astromodels --cov-report=xml
               env:
                   OMP_NUM_THREADS: 1
                   MKL_NUM_THREADS: 1
@@ -174,33 +165,28 @@ jobs:
         runs-on: ${{ matrix.os }}
         strategy:
             matrix:
-                os: [ubuntu-latest, macos-latest]
+                os: [ubuntu-latest, macos-latest, macos-13]
                 python-version: [3.9]
-
+                include:
+                  - environment: ci/environment.yml
+                  - environment:  ci/environment_noxspec.yml
+                    os: macos-latest
         steps:
             - name: Checkout
               uses: actions/checkout@v4
               with:
                   fetch-depth: 0
-            - name: Cache conda
-              uses: actions/cache@v4
-              env:
-                # Increase this value to reset cache if etc/example-environment.yml has not changed
-                CACHE_NUMBER: 0
-              with:
-                  path: ~/conda_pkgs_dir
-                  key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('ci/environment.yml') }}
             - name: Add conda ${{ matrix.python-version }} to system path
               uses: conda-incubator/setup-miniconda@v3
               with:
                   activate-environment: "test_env"
                   auto-activate-base: false
-                  architecture: "x64"
-                  miniforge-variant: Mambaforge
+                  #architecture: "x64"
+                  miniforge-variant: Miniforge3
                   #miniforge-version: latest
                   python-version: ${{ matrix.python-version }}
                   auto-update-conda: true
-                  environment-file: ci/environment.yml
+                  environment-file: ${{ matrix.environment }}
                   use-only-tar-bz2: true
                   channel-priority: true
                   channels: conda-forge, xspecmodels, threeml
@@ -254,12 +240,16 @@ jobs:
                   LABEL="--label dev"
 
                   fi
-
                   if [[ ${{matrix.os}} == ubuntu-latest ]];
                   then
 
                   anaconda -v --show-traceback -t $UPLOAD_TOKEN upload -u threeml ${CONDA}/envs/test_env/conda-bld/linux-64/*.tar.bz2 --force $LABEL
 
+                  elif [[ ${{matrix.os}} == macos-latest ]];
+                  then
+
+                  anaconda -v --show-traceback -t $UPLOAD_TOKEN upload -u threeml ${CONDA}/envs/test_env/conda-bld/osx-arm64/*.tar.bz2 --force $LABEL
+
                   else
 
                   anaconda -v --show-traceback -t $UPLOAD_TOKEN upload -u threeml ${CONDA}/envs/test_env/conda-bld/osx-64/*.tar.bz2 --force $LABEL

.github/workflows/docs.yml

@@ -48,7 +48,8 @@ jobs:
       - name: Execute the notebooks
         #shell: bash -l {0}
         run: |
-
+          # Make sure we fail in case of error
+          set -e
           # Download an example file
           
           wget https://www.astropy.org/astropy-data/photometry/spitzer_example_image.fits

.github/workflows/test_and_build.yml

@@ -37,7 +37,7 @@ jobs:
             fail-fast: false
             matrix:
                 python-version: ["3.9", "3.10", "3.11"]
-                os: ["ubuntu-latest", "macos-latest", "macos-12"]
+                os: ["ubuntu-latest", "macos-latest", "macos-13"]
         runs-on: ${{ matrix.os }}
         steps:
             - name: Checkout
@@ -100,36 +100,28 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                os: ["ubuntu-latest", "macos-latest", "macos-12"]
+                os: ["ubuntu-latest", "macos-latest", "macos-13"]
                 python-version: [3.9]
+                include:
+                  - environment: ci/environment.yml
+                  - environment:  ci/environment_noxspec.yml
+                    os: macos-latest
         runs-on: ${{ matrix.os }}
         steps:
             - name: Checkout
               uses: actions/checkout@v4
-            # - name: Cache conda
-            #   uses: actions/cache@v4
-            #   env:
-            #     # Increase this value to reset cache if etc/example-environment.yml has not changed
-            #     CACHE_NUMBER: 0
-            #   with:
-            #       path: ~/conda_pkgs_dir
-            #       key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('ci/environment.yml') }}
             - name: Add conda ${{ matrix.python-version }} to system path
               uses: conda-incubator/setup-miniconda@v3
               with:
                   activate-environment: "test_env"
                   auto-activate-base: false
-                  architecture: "x64"
-                  #mamba-version: "*"
                   miniforge-version: latest
                   python-version: ${{ matrix.python-version }}
                   auto-update-conda: true
-                  environment-file: ci/environment.yml
+                  environment-file: ${{ matrix.environment }}
                   use-only-tar-bz2: true
                   channel-priority: strict
                   channels: conda-forge, xspecmodels
-
-
             - name: Init Env
               shell: bash -l {0}
               run: |
@@ -166,14 +158,13 @@ jobs:
                   # stop the build if there are Python syntax errors or undefined names
                   flake8
 
-            - name: Test conda install
+            - name: Test import xspec
+              if: matrix.os != 'macos-latest'
               shell: bash -l {0}
-              run: |
-              
-                  echo "======>  importing XSPEC..."
-                  python -c "import astromodels.xspec"
-                  python -m pytest -vv --cov=astromodels --cov-report=xml
-
+              run: python -c "import astromodels.xspec"
+            - name: Test astromodels
+              shell: bash -l {0}
+              run: python -m pytest -vv --cov=astromodels --cov-report=xml
               env:
                   OMP_NUM_THREADS: 1
                   MKL_NUM_THREADS: 1

astromodels/functions/function.py

@@ -24,6 +24,7 @@
 from astromodels.utils.logging import setup_logger
 from astromodels.utils.pretty_list import dict_to_list
 from astromodels.utils.table import dict_to_table
+from astromodels.utils.file_utils import copy_if_needed
 from yaml.reader import ReaderError
 
 log = setup_logger(__name__)
@@ -1479,7 +1480,7 @@ def __call__(self, x):
 
             # Transform the input to an array of floats. If x is a single number, this will be an array of size 1
 
-            new_input = np.array(x, dtype=float, ndmin=1, copy=False)
+            new_input = np.array(x, dtype=float, ndmin=1, copy=copy_if_needed)
 
             # Compute the function
 
@@ -1705,8 +1706,8 @@ def __call__(self, x, y, *args, **kwargs):
 
             # Transform the input to an array of floats
 
-            new_x = np.array(x, dtype=float, ndmin=1, copy=False)
-            new_y = np.array(y, dtype=float, ndmin=1, copy=False)
+            new_x = np.array(x, dtype=float, ndmin=1, copy=copy_if_needed)
+            new_y = np.array(y, dtype=float, ndmin=1, copy=copy_if_needed)
 
             # Compute the function
 
@@ -1876,9 +1877,9 @@ def __call__(self, x, y, z):
             # This is either a single number or a list
             # Transform the input to an array of floats
 
-            new_x = np.array(x, dtype=float, ndmin=1, copy=False)
-            new_y = np.array(y, dtype=float, ndmin=1, copy=False)
-            new_z = np.array(z, dtype=float, ndmin=1, copy=False)
+            new_x = np.array(x, dtype=float, ndmin=1, copy=copy_if_needed)
+            new_y = np.array(y, dtype=float, ndmin=1, copy=copy_if_needed)
+            new_z = np.array(z, dtype=float, ndmin=1, copy=copy_if_needed)
 
             # Compute the function
 

astromodels/functions/functions_1D/extinction.py

@@ -9,6 +9,7 @@
 
 from astromodels.functions.function import Function1D, FunctionMeta
 from astromodels.utils.logging import setup_logger
+from astromodels.utils.file_utils import copy_if_needed
 
 log = setup_logger(__name__)
 
@@ -89,7 +90,7 @@ def evaluate(self, x, e_bmv, rv, redshift):
 
         if isinstance(x, astropy_units.Quantity):
 
-            _x = np.array(x.to("keV").value, ndmin=1, copy=False, dtype=float)
+            _x = np.array(x.to("keV").value, ndmin=1, copy=copy_if_needed, dtype=float)
 
             _unit = astropy_units.cm**2
             _y_unit = astropy_units.dimensionless_unscaled

astromodels/functions/template_model.py

@@ -20,6 +20,7 @@
 from astromodels.functions.function import Function1D, FunctionMeta
 from astromodels.utils import get_user_data_path
 from astromodels.utils.logging import setup_logger
+from astromodels.utils.file_utils import copy_if_needed
 
 log = setup_logger(__name__)
 
@@ -760,7 +761,7 @@ def _interpolate(self, energies, scale, parameters_values):
             # the logarithm below will fail.
 
             energies = np.array(
-                energies.to("keV").value, ndmin=1, copy=False, dtype=float
+                energies.to("keV").value, ndmin=1, copy=copy_if_needed, dtype=float
             )
 
             # Same for the scale

astromodels/utils/file_utils.py

@@ -3,11 +3,19 @@
 
 import os
 from pathlib import Path
-
+from typing import Optional
+import numpy as np
 import pkg_resources
 
 _custom_config_path = os.environ.get("ASTROMODELS_CONFIG")
 
+copy_if_needed: Optional[bool]
+
+if np.lib.NumpyVersion(np.__version__) >= "2.0.0":
+    copy_if_needed = None
+else:
+    copy_if_needed = False
+
 
 def _get_data_file_path(data_file: str) -> Path:
     """

astromodels/xspec/factory.py

@@ -431,6 +431,7 @@ def get_models(model_dat_path):
 from astromodels.functions.function import FunctionMeta, Function1D
 import numpy as np
 import astropy.units as u
+from astromodels.utils.file_utils import copy_if_needed
 from astromodels.xspec import _xspec
 import six
 
@@ -486,7 +487,7 @@ def evaluate(self, x, $PARAMETERS_NAMES$):
 
         if isinstance(x, u.Quantity):
 
-            x = np.array(x.to('keV').value, ndmin=1, copy=False, dtype=float)
+            x = np.array(x.to('keV').value, ndmin=1, copy=copy_if_needed, dtype=float)
 
             quantity = True
 

ci/environment_noxspec.yml

@@ -0,0 +1,27 @@
+name: test_env
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+  - python
+  - numpy
+  - pyyaml>=5.1
+  - astropy
+  - scipy
+  - numdifftools
+  - hdf5
+  - pytables
+  - pandas>=0.23
+  - dill
+  - wcslib
+  - future
+  - numba
+  - h5py
+  - interpolation>=2.2.3
+  - libgfortran
+  - omegaconf
+  - colorama
+  - rich
+  - joblib

conda-dist/recipe/meta.yaml

@@ -13,10 +13,10 @@ requirements:
     - {{ compiler('c') }} # [linux]
     - {{ compiler('cxx') }} # [linux]
     - {{ compiler('fortran') }} # [linux]
-    - xspec-modelsonly
-    - cfitsio
-    - ccfits
-    - wcslib
+    - xspec-modelsonly #[not arm64]
+    - cfitsio # [not arm64]
+    - ccfits # [not arm64]
+    - wcslib # [not arm64]
 
   host:
     - python
@@ -25,10 +25,10 @@ requirements:
     - numpy
     - pyyaml>=5.1
     - pandas>=0.23
-    - cfitsio
-    - ccfits
-    - wcslib
-    - xspec-modelsonly
+    - cfitsio # [not arm64]
+    - ccfits # [not arm64]
+    - wcslib # [not arm64]
+    - xspec-modelsonly # [not arm64]
     - future
     - numba>=0.54
     - h5py
@@ -46,9 +46,9 @@ requirements:
     - pytables
     - pandas>=0.23
     - dill
-    - cfitsio
-    - ccfits
-    - wcslib
+    - cfitsio # [not arm64]
+    - ccfits # [not arm64]
+    - wcslib # [not arm64]
     - future
     - numba>=0.54
     - h5py