Jammy2211 · Jammy2211 · Dec 16, 2024
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,92 +1,92 @@
-name: Tests
-
-on: [push, pull_request]
-
-jobs:
-  unittest:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.9, '3.10', '3.11', '3.12']
-    steps:
-    - name: Checkout PyAutoConf
-      uses: actions/checkout@v2
-      with:
-        repository: rhayes777/PyAutoConf
-        path: PyAutoConf
-    - name: Checkout PyAutoArray
-      uses: actions/checkout@v2
-      with:
-        path: PyAutoArray
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - uses: actions/cache@v2
-      id: cache-pip
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
-    - name: Install dependencies
-   #   if: steps.cache-pip.outputs.cache-hit != 'true'
-      run: |
-        pip3 install --upgrade pip
-        pip3 install setuptools
-        pip3 install wheel
-        pip3 install pytest coverage pytest-cov
-        pip3 install -r PyAutoConf/requirements.txt
-        pip3 install -r PyAutoArray/requirements.txt
-        pip3 install -r PyAutoArray/optional_requirements.txt
-
-        cd PyAutoArray/autoarray/util/nn/src/nn
-        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/runner/work/PyAutoArray/PyAutoArray/PyAutoArray/autoarray/util/nn/src/nn
-        bash ./configure
-        cp makefile_autolens makefile
-        make
-        cd /home/runner/work/PyAutoArray/PyAutoArray
-
-    - name: Extract branch name
-      shell: bash
-      run: |
-        cd PyAutoArray
-        echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
-      id: extract_branch
-    - name: Change to same branch if exists in deps
-      shell: bash
-      run: |
-        export PACKAGES=("PyAutoConf")
-        export BRANCH="${{ steps.extract_branch.outputs.branch }}"
-        for PACKAGE in ${PACKAGES[@]}; do
-          pushd $PACKAGE
-          export existed_in_remote=$(git ls-remote --heads origin ${BRANCH})
-          if [[ -z ${existed_in_remote} ]]; then
-            echo "Branch $BRANCH did not exist in $PACKAGE"
-          else
-            echo "Branch $BRANCH did exist in $PACKAGE"
-            git fetch
-            git checkout $BRANCH
-          fi
-          popd
-        done
-    - name: Run tests
-      run: |
-        export ROOT_DIR=`pwd`
-        export PYTHONPATH=$PYTHONPATH:$ROOT_DIR/PyAutoConf
-        export PYTHONPATH=$PYTHONPATH:$ROOT_DIR/PyAutoArray
-        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/runner/work/PyAutoArray/PyAutoArray/PyAutoArray/autoarray/util/nn/src/nn
-        pushd PyAutoArray
-        python3 -m pytest --cov autoarray --cov-report xml:coverage.xml
-    - name: Slack send
-      if: ${{ failure() }}
-      id: slack
-      uses: slackapi/slack-github-action@v1.21.0
-      env:
-        SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
-      with:
-        channel-id: C03S98FEDK2
-        payload: |
-                {
-                  "text": "${{ github.repository }}/${{ github.ref_name }} (Python ${{ matrix.python-version }}) build result: ${{ job.status }}\n${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}"
+name: Tests
+
+on: [push, pull_request]
+
+jobs:
+  unittest:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.9, '3.10', '3.11', '3.12']
+    steps:
+    - name: Checkout PyAutoConf
+      uses: actions/checkout@v2
+      with:
+        repository: rhayes777/PyAutoConf
+        path: PyAutoConf
+    - name: Checkout PyAutoArray
+      uses: actions/checkout@v2
+      with:
+        path: PyAutoArray
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/cache@v2
+      id: cache-pip
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+    - name: Install dependencies
+   #   if: steps.cache-pip.outputs.cache-hit != 'true'
+      run: |
+        pip3 install --upgrade pip
+        pip3 install setuptools
+        pip3 install wheel
+        pip3 install pytest coverage pytest-cov
+        pip3 install -r PyAutoConf/requirements.txt
+        pip3 install -r PyAutoArray/requirements.txt
+        pip3 install -r PyAutoArray/optional_requirements.txt
+
+        cd PyAutoArray/autoarray/util/nn/src/nn
+        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/runner/work/PyAutoArray/PyAutoArray/PyAutoArray/autoarray/util/nn/src/nn
+        bash ./configure
+        cp makefile_autolens makefile
+        make
+        cd /home/runner/work/PyAutoArray/PyAutoArray
+
+    - name: Extract branch name
+      shell: bash
+      run: |
+        cd PyAutoArray
+        echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+      id: extract_branch
+    - name: Change to same branch if exists in deps
+      shell: bash
+      run: |
+        export PACKAGES=("PyAutoConf")
+        export BRANCH="${{ steps.extract_branch.outputs.branch }}"
+        for PACKAGE in ${PACKAGES[@]}; do
+          pushd $PACKAGE
+          export existed_in_remote=$(git ls-remote --heads origin ${BRANCH})
+          if [[ -z ${existed_in_remote} ]]; then
+            echo "Branch $BRANCH did not exist in $PACKAGE"
+          else
+            echo "Branch $BRANCH did exist in $PACKAGE"
+            git fetch
+            git checkout $BRANCH
+          fi
+          popd
+        done
+    - name: Run tests
+      run: |
+        export ROOT_DIR=`pwd`
+        export PYTHONPATH=$PYTHONPATH:$ROOT_DIR/PyAutoConf
+        export PYTHONPATH=$PYTHONPATH:$ROOT_DIR/PyAutoArray
+        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/runner/work/PyAutoArray/PyAutoArray/PyAutoArray/autoarray/util/nn/src/nn
+        pushd PyAutoArray
+        python3 -m pytest --cov autoarray --cov-report xml:coverage.xml
+    - name: Slack send
+      if: ${{ failure() }}
+      id: slack
+      uses: slackapi/slack-github-action@v1.21.0
+      env:
+        SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
+      with:
+        channel-id: C03S98FEDK2
+        payload: |
+                {
+                  "text": "${{ github.repository }}/${{ github.ref_name }} (Python ${{ matrix.python-version }}) build result: ${{ job.status }}\n${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}"
                 }
diff --git a/autoarray/config/general.yaml b/autoarray/config/general.yaml
@@ -1,18 +1,18 @@
-fits:
-  flip_for_ds9: false                 # If True, the image is flipped before output to a .fits file, which is useful for viewing in DS9.
-inversion:
-  check_reconstruction: true          # If True, the inversion's reconstruction is checked to ensure the solution of a meshs's mapper is not an invalid solution where the values are all the same.
-  use_positive_only_solver: true      # If True, inversion's use a positive-only linear algebra solver by default, which is slower but prevents unphysical negative values in the reconstructed solutuion.
-  no_regularization_add_to_curvature_diag_value : 1.0e-3 # The default value added to the curvature matrix's diagonal when regularization is not applied to a linear object, which prevents inversion's failing due to the matrix being singular.
-  positive_only_uses_p_initial: true  # If True, the positive-only solver of an inversion's uses an initial guess of the reconstructed data's values as which values should be positive, speeding up the solver.
-  use_border_relocator: false          # If True, by default a pixelization's border is used to relocate all pixels outside its border to the border.
-  reconstruction_vmax_factor: 0.5     # Plots of an Inversion's reconstruction use the reconstructed data's bright value multiplied by this factor.
-numba:
-  use_numba: true
-  cache: false
-  nopython: true
-  parallel: false
-pixelization:
-  voronoi_nn_max_interpolation_neighbors: 300
-structures:
-  native_binned_only: false           # If True, data structures are only stored in their native and binned format. This is used to reduce memory usage in autocti.
+fits:
+  flip_for_ds9: false                 # If True, the image is flipped before output to a .fits file, which is useful for viewing in DS9.
+inversion:
+  check_reconstruction: true          # If True, the inversion's reconstruction is checked to ensure the solution of a meshs's mapper is not an invalid solution where the values are all the same.
+  use_positive_only_solver: true      # If True, inversion's use a positive-only linear algebra solver by default, which is slower but prevents unphysical negative values in the reconstructed solutuion.
+  no_regularization_add_to_curvature_diag_value : 1.0e-3 # The default value added to the curvature matrix's diagonal when regularization is not applied to a linear object, which prevents inversion's failing due to the matrix being singular.
+  positive_only_uses_p_initial: true  # If True, the positive-only solver of an inversion's uses an initial guess of the reconstructed data's values as which values should be positive, speeding up the solver.
+  use_border_relocator: false          # If True, by default a pixelization's border is used to relocate all pixels outside its border to the border.
+  reconstruction_vmax_factor: 0.5     # Plots of an Inversion's reconstruction use the reconstructed data's bright value multiplied by this factor.
+numba:
+  use_numba: true
+  cache: false
+  nopython: true
+  parallel: false
+pixelization:
+  voronoi_nn_max_interpolation_neighbors: 300
+structures:
+  native_binned_only: false           # If True, data structures are only stored in their native and binned format. This is used to reduce memory usage in autocti.
diff --git a/autoarray/config/grids.yaml b/autoarray/config/grids.yaml
@@ -1,3 +1,3 @@
-radial_minimum:
-  function_name:
-    class_name: 1.0e-08
+radial_minimum:
+  function_name:
+    class_name: 1.0e-08
diff --git a/autoarray/config/logging.yaml b/autoarray/config/logging.yaml
@@ -1,22 +1,22 @@
-version: 1
-disable_existing_loggers: false
-
-handlers:
-  console:
-    class: logging.StreamHandler
-    level: INFO
-    stream: ext://sys.stdout
-    formatter: formatter
-  file:
-    class: logging.FileHandler
-    level: INFO
-    filename: root.log
-    formatter: formatter
-
-root:
-  level: INFO
-  handlers: [ console, file ]
-
-formatters:
-  formatter:
-    format: '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
+version: 1
+disable_existing_loggers: false
+
+handlers:
+  console:
+    class: logging.StreamHandler
+    level: INFO
+    stream: ext://sys.stdout
+    formatter: formatter
+  file:
+    class: logging.FileHandler
+    level: INFO
+    filename: root.log
+    formatter: formatter
+
+root:
+  level: INFO
+  handlers: [ console, file ]
+
+formatters:
+  formatter:
+    format: '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
diff --git a/autoarray/numpy_wrapper.py b/autoarray/numpy_wrapper.py
@@ -1,37 +1,37 @@
-import logging
-
-from os import environ
-
-use_jax = environ.get("USE_JAX", "0") == "1"
-
-if use_jax:
-    try:
-        import jax
-        from jax import numpy as np, jit
-
-        print("JAX mode enabled")
-    except ImportError:
-        raise ImportError(
-            "JAX is not installed. Please install it with `pip install jax`."
-        )
-else:
-    import numpy as np
-
-    def jit(function, *_, **__):
-        return function
-
-
-try:
-    from jax._src.tree_util import register_pytree_node
-    from jax._src.tree_util import register_pytree_node_class
-
-    from jax import Array
-except ImportError:
-
-    def register_pytree_node_class(cls):
-        return cls
-
-    def register_pytree_node(*_, **__):
-        pass
-
-    Array = np.ndarray
+import logging
+
+from os import environ
+
+use_jax = environ.get("USE_JAX", "0") == "1"
+
+if use_jax:
+    try:
+        import jax
+        from jax import numpy as np, jit
+
+        print("JAX mode enabled")
+    except ImportError:
+        raise ImportError(
+            "JAX is not installed. Please install it with `pip install jax`."
+        )
+else:
+    import numpy as np
+
+    def jit(function, *_, **__):
+        return function
+
+
+try:
+    from jax._src.tree_util import register_pytree_node
+    from jax._src.tree_util import register_pytree_node_class
+
+    from jax import Array
+except ImportError:
+
+    def register_pytree_node_class(cls):
+        return cls
+
+    def register_pytree_node(*_, **__):
+        pass
+
+    Array = np.ndarray
diff --git a/autoarray/structures/arrays/kernel_2d.py b/autoarray/structures/arrays/kernel_2d.py
@@ -52,7 +52,7 @@ def __init__(
         )
 
         if normalize:
-            self._array[:] = np.divide(self._array, np.sum(self._array))
+            self._array = np.divide(self._array, np.sum(self._array))
 
     @classmethod
     def no_mask(
@@ -84,7 +84,7 @@ def no_mask(
             If True, the Kernel2D's array values are normalized such that they sum to 1.0.
         """
         values = Array2D.no_mask(
-            values=values,
+            values=values.array,
             shape_native=shape_native,
             pixel_scales=pixel_scales,
             origin=origin,