Merge branch 'activ_dev' of https://github.com/exoAtmospheres/ForMoSA …

…into activ_dev

.github/workflows/codeql.yml

@@ -0,0 +1,93 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "activ_dev", "main*" ]
+  pull_request:
+    branches: [ "activ_dev", "main*" ]
+  schedule:
+    - cron: '24 12 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: python
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+    - if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        exit 1
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

readthedocs.yml → .readthedocs.yaml

@@ -8,13 +8,26 @@ version: 2
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/source/conf.py
+   configuration: docs/conf.py
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
    install:
    - requirements: requirements.txt
-   system_packages: True
-
-submodules:
-   include: all
+   - requirements: docs/requirements.txt
+#   system_packages: True
+#   
+#submodules:
+#   include: all

ForMoSA.egg-info/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: ForMoSA
-Version: 2.0.0
+Version: 1.1.3
 Summary: ForMoSA: Forward Modeling Tool for Spectral Analysis
 Home-page: https://github.com/exoAtmospheres/ForMoSA
 Author: P. Palma-Bifani, S. Petrus, M. Ravet, A. Denis, M. Bonnefoy, G. Chauvin
 Author-email: [email protected]
-License: BSD 2-Clause License
+License: BSD 3-Clause License
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: matplotlib
@@ -18,5 +18,11 @@ Requires-Dist: nestle
 Requires-Dist: PyAstronomy
 Requires-Dist: spectres
 Requires-Dist: pyyaml
+Requires-Dist: tqdm
 Requires-Dist: importlib-metadata==4.13.0
 Requires-Dist: xarray==2023.10.1
+
+Welcome to ForMoSA, an open-source Python package. 
+We designed this tool to model exoplanetary atmospheres with a forward modeling approach. 
+
+We encourage the community to exploit its capabilities!

ForMoSA.egg-info/requires.txt

@@ -9,5 +9,6 @@ nestle
 PyAstronomy
 spectres
 pyyaml
+tqdm
 importlib-metadata==4.13.0
 xarray==2023.10.1

ForMoSA/__init__.py

@@ -1,5 +1,5 @@
 import os
 
-__version__ = "2.0.0"
+__version__ = "1.1.3"
 
 __all__ = ['adapt', 'nested_sampling','plotting']

ForMoSA/adapt/adapt_grid.py

@@ -2,7 +2,9 @@
 import numpy as np
 import xarray as xr
 import time
-import os
+import os, sys
+
+sys.path.insert(0, os.path.abspath('../'))
 
 from adapt.extraction_functions import adapt_model, decoupe
 
@@ -15,15 +17,15 @@ def adapt_grid(global_params, wav_obs_spectro, wav_obs_photo, res_mod_obs_merge,
     Adapt the synthetic spectra of a grid to make them comparable with the data.
     
     Args:
-        global_params (object): Class containing each parameter
+        global_params    (object): Class containing each parameter
         wav_obs_spectro   (array): Merged wavelength grid of the data
         wav_obs_photo     (array): Wavelengths of the photometry points
         obs_name            (str): Name of the current observation looping
         indobs              (int): Index of the current observation looping
     Returns:
         None
 
-    Author: Simon Petrus / Adapted: Matthieu Ravet & Paulina Palma-Bifani
+    Author: Simon Petrus, Matthieu Ravet and Paulina Palma-Bifani
     """
 
     ds = xr.open_dataset(global_params.model_path, decode_cf=False, engine="netcdf4")

ForMoSA/adapt/adapt_obs_mod.py

@@ -1,14 +1,15 @@
 from __future__ import print_function, division
 import numpy as np
-import os
+import os,sys
 import xarray as xr
 from scipy.interpolate import interp1d
 
+sys.path.insert(0, os.path.abspath('../'))
+
 from adapt.extraction_functions import extract_observation
 from adapt.adapt_grid import adapt_grid
 from main_utilities import diag_mat
 import glob
-# import matplotlib.pyplot as plt
 # ----------------------------------------------------------------------------------------------------------------------
 
 
@@ -22,7 +23,7 @@ def launch_adapt(global_params, justobs='no'):
     Returns:
         None
 
-    Author: Simon Petrus / Adapted: Matthieu Ravet, Paulina Palma-Bifani and Allan Denis
+    Author: Simon Petrus, Matthieu Ravet, Paulina Palma-Bifani and Allan Denis
     """
 
     # Get back the grid information from the config file