specula 1.0.0a10__tar.gz → 1.0.1__tar.gz

{specula-1.0.0a10 → specula-1.0.1}/.github/workflows/publish.yml

@@ -10,6 +10,10 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: read
+      id-token: write  # OIDC AUTHENTICATION
+    # Run only on:
+    # - tag pushes
+    # - PRs with label "Build wheels"
     if: >
       (github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) ||
       contains(toJson(github.event.pull_request.labels), 'Build wheels')
@@ -26,15 +30,6 @@ jobs:
         run: python -m build --sdist --wheel .
       - name: List result
         run: ls -l dist
-      - name: Publish pre-release 📦 to TestPyPI
-        if: startsWith(github.ref, 'refs/tags') && (contains(github.ref, 'a') || contains(github.ref, 'b') || contains(github.ref, 'rc') || contains(github.ref, '-'))
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
-        run: python -m twine upload --repository testpypi dist/*
       - name: Publish distribution 📦 to PyPI
-        if: startsWith(github.ref, 'refs/tags') && !contains(github.ref, 'a') && !contains(github.ref, 'b') && !contains(github.ref, 'rc') && !contains(github.ref, '-')
-        env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-        run: python -m twine upload dist/*
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1

specula-1.0.1/.github/workflows/pythonpackage.yml

@@ -0,0 +1,68 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+#  schedule:
+#    - cron: "1 1 * * *"
+
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+
+    - name: Install dependencies
+      run: |
+        bash
+        if ${{runner.os == 'Linux'}}; then
+          sudo apt update
+          sudo apt install libcairo2-dev pkg-config python3-dev
+        fi
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install pytest pytest-cov flake8
+
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+    - name: Test with pytest and generate coverage report
+      run: |
+        pytest --cov=./ --cov-report=xml
+
+    - name: Upload coverage to Codecov
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+        flags: unittests
+        override_branch: ${{ github.head_ref || github.ref_name }}
+        override_commit: ${{ github.sha }}
+        fail_ci_if_error: false
+        verbose: true

{specula-1.0.0a10 → specula-1.0.1}/.readthedocs.yaml

@@ -20,4 +20,5 @@ sphinx:
 python:
    install:
    - requirements: docs/requirements.txt
-        
+   - method: pip
+     path: .

{specula-1.0.0a10 → specula-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: specula
-Version: 1.0.0a10
+Version: 1.0.1
 Summary: PYramid Simulator Software for Adaptive OpTics Arcetri
 Author: Alfio Puglisi, Guido Agapito, INAF Arcetri Adaptive Optics group
 Author-email: Fabio Rossi <fabio.rossi@inaf.it>
@@ -22,7 +22,6 @@ Requires-Dist: flask-socketio
 Requires-Dist: python-socketio
 Requires-Dist: requests
 Requires-Dist: pytest
-Requires-Dist: scikit-image
 Provides-Extra: control
 Requires-Dist: control; extra == "control"
 Provides-Extra: diagrams
@@ -44,8 +43,9 @@ See the documentation here: [specula.readthedocs.io](https://specula.readthedocs
 ## Directories
 
 - **docs**: contains the documentation.
-- **main**: contains functions and parameter files to calibrate and run a closed loop of an adaptive optics system (single-conjugated, multi-conjugated, natural, laser, ...).
+- **config**: contains functions and parameter files to calibrate and run a closed loop of an adaptive optics system (single-conjugated, multi-conjugated, natural, laser, ...).
 - **specula**: the main library, structured as follows:
+  - **data**: data required by utility functions.
   - **data_objects**: classes that wrap the data and provide methods to access them.
   - **display**: classes for data visualization.
   - **lib**: utility functions used by multiple objects.
@@ -62,22 +62,14 @@ See the documentation here: [specula.readthedocs.io](https://specula.readthedocs
 - flask
 - flask-socketio
 - socketio
-- scikit-image (for physical propagation)
 - cupy (for GPU acceleration, optional)
 
 ### Optional libraries
 
 Some features require additional libraries:
-- **pycairo**: needed for block diagram generation with orthogram
-- **orthogram**: for automatic block diagram creation (see [orthogram](https://pypi.org/project/orthogram/))
+- **orthogram**: for automatic block diagram creation (see [orthogram](https://pypi.org/project/orthogram/), requires **pycairo**)
 - **control**: for conversion of transfer function system in SPECULA format and vice-versa and analysis of transfer function
 
-Install optional dependencies (pycairo will be installed as dependency of orthogram) with:
-```bash
-pip install orthogram
-pip install control
-```
-
 ## Contributing to SPECULA
 To contribute to SPECULA, follow these steps:
 
@@ -89,3 +81,22 @@ To contribute to SPECULA, follow these steps:
 6. Create the pull request.
 
 We require tests for all new features to ensure the stability of the project.
+
+## Citation
+
+If you use SPECULA in your research, please cite:
+
+```bibtex
+@article{specula2026,
+  author = {Fabio Rossi and Alfio Puglisi and Guido Agapito},
+  title = {{Introducing a new generation adaptive optics simulation framework: from PASSATA to SPECULA}},
+  volume = {12},
+  journal = {Journal of Astronomical Telescopes, Instruments, and Systems},
+  number = {1},
+  publisher = {SPIE},
+  pages = {019001},
+  year = {2026},
+  doi = {10.1117/1.JATIS.12.1.019001},
+  URL = {https://doi.org/10.1117/1.JATIS.12.1.019001}
+}
+```

{specula-1.0.0a10 → specula-1.0.1}/README.md

@@ -10,8 +10,9 @@ See the documentation here: [specula.readthedocs.io](https://specula.readthedocs
 ## Directories
 
 - **docs**: contains the documentation.
-- **main**: contains functions and parameter files to calibrate and run a closed loop of an adaptive optics system (single-conjugated, multi-conjugated, natural, laser, ...).
+- **config**: contains functions and parameter files to calibrate and run a closed loop of an adaptive optics system (single-conjugated, multi-conjugated, natural, laser, ...).
 - **specula**: the main library, structured as follows:
+  - **data**: data required by utility functions.
   - **data_objects**: classes that wrap the data and provide methods to access them.
   - **display**: classes for data visualization.
   - **lib**: utility functions used by multiple objects.
@@ -28,22 +29,14 @@ See the documentation here: [specula.readthedocs.io](https://specula.readthedocs
 - flask
 - flask-socketio
 - socketio
-- scikit-image (for physical propagation)
 - cupy (for GPU acceleration, optional)
 
 ### Optional libraries
 
 Some features require additional libraries:
-- **pycairo**: needed for block diagram generation with orthogram
-- **orthogram**: for automatic block diagram creation (see [orthogram](https://pypi.org/project/orthogram/))
+- **orthogram**: for automatic block diagram creation (see [orthogram](https://pypi.org/project/orthogram/), requires **pycairo**)
 - **control**: for conversion of transfer function system in SPECULA format and vice-versa and analysis of transfer function
 
-Install optional dependencies (pycairo will be installed as dependency of orthogram) with:
-```bash
-pip install orthogram
-pip install control
-```
-
 ## Contributing to SPECULA
 To contribute to SPECULA, follow these steps:
 
@@ -55,3 +48,22 @@ To contribute to SPECULA, follow these steps:
 6. Create the pull request.
 
 We require tests for all new features to ensure the stability of the project.
+
+## Citation
+
+If you use SPECULA in your research, please cite:
+
+```bibtex
+@article{specula2026,
+  author = {Fabio Rossi and Alfio Puglisi and Guido Agapito},
+  title = {{Introducing a new generation adaptive optics simulation framework: from PASSATA to SPECULA}},
+  volume = {12},
+  journal = {Journal of Astronomical Telescopes, Instruments, and Systems},
+  number = {1},
+  publisher = {SPIE},
+  pages = {019001},
+  year = {2026},
+  doi = {10.1117/1.JATIS.12.1.019001},
+  URL = {https://doi.org/10.1117/1.JATIS.12.1.019001}
+}
+```

{specula-1.0.0a10 → specula-1.0.1}/docs/api/data_objects.rst

@@ -184,6 +184,15 @@ Source
    :show-inheritance:
 
 
+Ssr Filter Data
+---------------
+
+.. automodule:: specula.data_objects.ssr_filter_data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Subap Data
 ----------
 

{specula-1.0.0a10 → specula-1.0.1}/docs/api/lib.rst

@@ -13,6 +13,15 @@ Elt M1 Ifunc Calculator
    :show-inheritance:
 
 
+Calc Geometry
+-------------
+
+.. automodule:: specula.lib.calc_geometry
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Calc Noise Cov Elong
 --------------------
 
@@ -94,6 +103,15 @@ Flatten
    :show-inheritance:
 
 
+Fsoc Lib
+--------
+
+.. automodule:: specula.lib.fsoc_lib
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Interp2D
 --------
 
@@ -130,6 +148,15 @@ Mask
    :show-inheritance:
 
 
+Mmse Reconstructor
+------------------
+
+.. automodule:: specula.lib.mmse_reconstructor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Modal Base Generator
 --------------------
 

{specula-1.0.0a10 → specula-1.0.1}/docs/api/processing_objects.rst

@@ -4,6 +4,24 @@ Processing Objects API
 Processing objects for simulating AO system components.
 
 
+Abstract Coronagraph
+--------------------
+
+.. automodule:: specula.processing_objects.abstract_coronagraph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Apodizer Coronagraph
+--------------------
+
+.. automodule:: specula.processing_objects.apodizer_coronagraph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Atmo Evolution
 --------------
 
@@ -13,6 +31,15 @@ Atmo Evolution
    :show-inheritance:
 
 
+Atmo Evolution Up Down
+----------------------
+
+.. automodule:: specula.processing_objects.atmo_evolution_up_down
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Atmo Infinite Evolution
 -----------------------
 
@@ -22,6 +49,15 @@ Atmo Infinite Evolution
    :show-inheritance:
 
 
+Atmo Infinite Evolution Up Down
+-------------------------------
+
+.. automodule:: specula.processing_objects.atmo_infinite_evolution_up_down
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Atmo Propagation
 ----------------
 
@@ -67,6 +103,15 @@ Base Operation
    :show-inheritance:
 
 
+Base Slicer
+-----------
+
+.. automodule:: specula.processing_objects.base_slicer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Ccd
 ---
 
@@ -85,6 +130,15 @@ Data Buffer
    :show-inheritance:
 
 
+Data Print
+----------
+
+.. automodule:: specula.processing_objects.data_print
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Data Source
 -----------
 
@@ -157,6 +211,24 @@ Electric Field Combinator
    :show-inheritance:
 
 
+Electric Field Reflection
+-------------------------
+
+.. automodule:: specula.processing_objects.electric_field_reflection
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Ext Source Pyramid
+------------------
+
+.. automodule:: specula.processing_objects.ext_source_pyramid
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Extended Source
 ---------------
 
@@ -166,6 +238,24 @@ Extended Source
    :show-inheritance:
 
 
+Focal Plane Filter
+------------------
+
+.. automodule:: specula.processing_objects.focal_plane_filter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Four Quadrant Coronagraph
+-------------------------
+
+.. automodule:: specula.processing_objects.four_quadrant_coronagraph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Gain Optimizer
 --------------
 
@@ -229,6 +319,15 @@ Low Pass Filter
    :show-inheritance:
 
 
+Lyot Coronagraph
+----------------
+
+.. automodule:: specula.processing_objects.lyot_coronagraph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Mirror Commands Combinator
 --------------------------
 
@@ -301,6 +400,15 @@ Multi Rec Calibrator
    :show-inheritance:
 
 
+Mvm
+---
+
+.. automodule:: specula.processing_objects.mvm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Optical Gain Estimator
 ----------------------
 
@@ -328,6 +436,15 @@ Poly Chrom Sh
    :show-inheritance:
 
 
+Poly Chrom Wfs
+--------------
+
+.. automodule:: specula.processing_objects.poly_chrom_wfs
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Poly Crom Pyramid
 -----------------
 
@@ -337,6 +454,15 @@ Poly Crom Pyramid
    :show-inheritance:
 
 
+Power Loss
+----------
+
+.. automodule:: specula.processing_objects.power_loss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Psf
 ---
 
@@ -454,6 +580,24 @@ Sn Calibrator
    :show-inheritance:
 
 
+Spot Monitor
+------------
+
+.. automodule:: specula.processing_objects.spot_monitor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Ssr Filter
+----------
+
+.. automodule:: specula.processing_objects.ssr_filter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Time History Generator
 ----------------------
 
@@ -472,6 +616,15 @@ Vibration Generator
    :show-inheritance:
 
 
+Vortex Coronagraph
+------------------
+
+.. automodule:: specula.processing_objects.vortex_coronagraph
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 Wave Generator
 --------------
 

{specula-1.0.0a10 → specula-1.0.1}/docs/conf.py

@@ -10,12 +10,24 @@ import os
 import sys
 import re
 sys.path.insert(0, os.path.abspath('..'))
-from specula.__version__ import __version__
 
 project = 'SPECULA'
 copyright = '2025, Fabio Rossi, Alfio Puglisi, Guido Agapito'
 author = 'Fabio Rossi, Alfio Puglisi, Guido Agapito'
 
+# Read version from _version.py (generated by setuptools_scm)
+try:
+    from specula._version import version as __version__
+except ImportError:
+    # fallback: read from pyproject.toml if _version.py is missing (e.g. on RTD)
+    try:
+        import tomllib
+    except ImportError:
+        import toml as tomllib
+    with open(os.path.join(os.path.dirname(__file__), '..', 'pyproject.toml'), 'rb') as f:
+        pyproject = tomllib.load(f)
+    __version__ = pyproject['project']['version']
+
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 

{specula-1.0.0a10 → specula-1.0.1}/docs/index.rst

@@ -21,6 +21,7 @@ Getting Started
 
    Installation <installation>
    Simulation basics <simulation_basics>
+   Simulation parameters <simulation_parameters>
    Running simulations <running_simulations>
    Diagrams <simul_diagrams>
    Calibration manager <calibration_manager>
@@ -35,6 +36,7 @@ Tutorials
    Deformable Mirror actuator step response tutorial <tutorials/step_response_tutorial>
    Field Analyser (deferred computation of PSF, modal analysis and phase cube) tutorial <tutorials/field_analyser_tutorial>
    Pyramid WFS calibration in partial correction regime tutorial <tutorials/pwfs_calib_pc_tutorial>
+   Generators for vibrations and time histories tutorial <tutorials/generators_tutorial>
 
 Developer Guide  
 ---------------

{specula-1.0.0a10 → specula-1.0.1}/docs/installation.rst

@@ -47,8 +47,19 @@ If you have a CUDA-compatible GPU and want to benefit from GPU acceleration, ins
 **Without GPU:**
    SPECULA will automatically fall back to CPU computation using NumPy. Performance will be slower but all functionality remains available.
 
-Step 3: Clone SPECULA Repository
---------------------------------
+Step 3: Install SPECULA
+-----------------------
+
+You can install SPECULA in two ways:
+
+**A) Install from PyPI (recommended for most users):**
+
+.. code-block:: bash
+
+   # Install SPECULA from PyPI
+   pip install specula
+
+**B) Install from source (for development or latest features):**
 
 Clone the SPECULA repository from GitHub:
 
@@ -56,24 +67,16 @@ Clone the SPECULA repository from GitHub:
 
    # Clone the repository
    git clone https://github.com/ArcetriAdaptiveOptics/SPECULA.git
-   
+
    # Navigate to the directory
    cd SPECULA
 
-**Alternative: Download ZIP**
-   If you don't have Git installed, you can download the repository as a ZIP file from the GitHub page and extract it.
-
-Step 4: Install SPECULA
------------------------
-
-Install SPECULA and its dependencies:
+Then install in development mode:
 
 .. code-block:: bash
 
-   # Install in development mode (recommended)
    pip install -e .
 
-
 This installs SPECULA in "editable" mode, allowing you to modify the code and see changes immediately.
 
 **Required Dependencies:**
@@ -86,7 +89,6 @@ All required dependencies will be installed automatically, including:
 * **flask**: Web framework for display server
 * **flask-socketio**: Real-time web communication
 * **python-socketio**: WebSocket client support
-* **scikit-image**: Image processing
 
 Optional Libraries
 ^^^^^^^^^^^^^^^^^^
@@ -104,8 +106,14 @@ To install these libraries, first install pkg-config and cairo with conda:
    # Install dependencies for optional diagram tools
    conda install -c conda-forge pkg-config cairo
 
+To ensure that the correct version of pycairo is installed, use conda:
+
+.. code-block:: bash
+
+   # Install pycairo version 1.21.0
+   conda install -c conda-forge pycairo=1.21.0
+
 and then install orthogram with pip.
-pycairo will be installed as an orthogram dependency.
 
 .. code-block:: bash
 

{specula-1.0.0a10 → specula-1.0.1}/docs/requirements.txt

@@ -6,3 +6,4 @@ sphinx_rtd_theme
 pydata_sphinx_theme
 myst-parser
 lxml_html_clean
+toml