Rename to pomme

.github/workflows/build-and-test.yaml

@@ -28,7 +28,7 @@ jobs:
           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: Install p3droslo from source
+      - name: Install pomme from source
         run: |
           pip install .
       - name: Test with pytest

.github/workflows/upload-to-anaconda.yaml

@@ -63,28 +63,28 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
 
-      - name: Install dependencies and p3droslo (try 1)
+      - name: Install dependencies and pomme (try 1)
         id: install_try1
         run: |
           sleep 5
           mamba install pytest>=7
-          mamba install -c freddeceuster p3droslo
+          mamba install -c freddeceuster pomme
 
-      - name: Install dependencies and p3droslo (try 2)
+      - name: Install dependencies and pomme (try 2)
         id: install_try2
         if: steps.install_try1.outcome == 'failure'
         run: |
           sleep 5
           mamba install pytest>=7
-          mamba install -c freddeceuster p3droslo
+          mamba install -c freddeceuster pomme
 
-      - name: Install dependencies and p3droslo (try 3)
+      - name: Install dependencies and pomme (try 3)
         id: install_try3
         if: steps.install_try2.outcome == 'failure'
         run: |
           sleep 5
           mamba install pytest>=7
-          mamba install -c freddeceuster p3droslo
+          mamba install -c freddeceuster pomme
     
 
       - name: Test with pytest

.github/workflows/upload-to-pypi.yaml

@@ -56,9 +56,9 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install pytest>=7
-      - name: Install p3droslo from PyPI
+      - name: Install pomme from PyPI
         run: |
-          pip install p3droslo
+          pip install pomme
       - name: Test with pytest
         run: |
           pytest

.readthedocs.yaml

@@ -16,7 +16,7 @@ build:
   tools:
     python: "3.9"
 
-# Install p3droslo
+# Install pomme
 python:
   install:
     - requirements: docs/src/requirements.txt

CONTRIBUTING.md

@@ -1,19 +1,19 @@
-# Contributing to p3droslo
+# Contributing to pomme
 
-Thank you for considering contributing to p3droslo!
+Thank you for considering contributing to pomme!
 We highly appreciate any efforts to improve our software.
-In case you have any suggestions, questions, possible bugs, or feature requests, please, open an issue [here](https://github.com/Magritte-code/p3droslo/issues).
+In case you have any suggestions, questions, possible bugs, or feature requests, please, open an issue [here](https://github.com/Magritte-code/pomme/issues).
 
 
 ## Contributing examples and use cases
 
-If you have used p3droslo in a way that is different from any of our [examples](https://p3droslo.readthedocs.io/en/latest/examples/index.html), we highly encourage you to contribute to the [examples](https://p3droslo.readthedocs.io/en/latest/examples/index.html) in the documentation.
+If you have used pomme in a way that is different from any of our [examples](https://pomme.readthedocs.io/en/latest/examples/index.html), we highly encourage you to contribute to the [examples](https://pomme.readthedocs.io/en/latest/examples/index.html) in the documentation.
 You can do this by preparing your example as a jupyter notebook and creating a pull request (see below). If you are unsure about your example or how to add it, please contact us and we can help.
 
 
 ## Contributing new functionality
 
-We have a clear development strategy for p3droslo which is closely related to our reseach. Several features are being developed for several projects, all of which might not yet be publicly visible. Therefore, to prevent development overlap, we advise to contact us (e.g. by creating an [issue](https://github.com/Magritte-code/p3droslo/issues)), before starting to work on p3droslo yourself. We are happy to share our preliminary features if they could help you, or welcome you to our develoment team to colaboratively work on our projects.
+We have a clear development strategy for pomme which is closely related to our reseach. Several features are being developed for several projects, all of which might not yet be publicly visible. Therefore, to prevent development overlap, we advise to contact us (e.g. by creating an [issue](https://github.com/Magritte-code/pomme/issues)), before starting to work on pomme yourself. We are happy to share our preliminary features if they could help you, or welcome you to our develoment team to colaboratively work on our projects.
 
 
 ## Contributing bug fixes
@@ -25,7 +25,7 @@ For bug fixes or smaller contributions, we gladly accept pull requests (see belo
 
 The advised procedure for creating pull requests for Magritte goes as follows:
 
-- Fork the p3droslo GitHub repository and create a new branch for your work;
+- Fork the pomme GitHub repository and create a new branch for your work;
 - Add your changes and commit them;
 - Add or modify the existing tests for your changes;
 - Verify if your new and all previous tests pass;

README.md

@@ -1,40 +1,40 @@
-# p3droslo
+# pomme
 
 _Probabilistic 3D Reconstruction of Spectral Line Observations._
 
 
-![Build status](https://github.com/Magritte-code/p3droslo/actions/workflows/build-and-test.yaml/badge.svg)
-![Build status](https://github.com/Magritte-code/p3droslo/actions/workflows/upload-to-pypi.yaml/badge.svg)
-![Build status](https://github.com/Magritte-code/p3droslo/actions/workflows/upload-to-anaconda.yaml/badge.svg)
+![Build status](https://github.com/Magritte-code/pomme/actions/workflows/build-and-test.yaml/badge.svg)
+![Build status](https://github.com/Magritte-code/pomme/actions/workflows/upload-to-pypi.yaml/badge.svg)
+![Build status](https://github.com/Magritte-code/pomme/actions/workflows/upload-to-anaconda.yaml/badge.svg)
 
 
 ## About
 
-*p3droslo* is a python package that allows you to create **probabilistic 3D reconstructions** of astronomical **spectral line observations**.
+*pomme* is a python package that allows you to create **probabilistic 3D reconstructions** of astronomical **spectral line observations**.
 
 Observations of [spectral lines](https://en.wikipedia.org/wiki/Spectral_line) are indespensible in astronomy, since they encode a wealth of information about the physical and chemical conditions of the medium from which they originate.
 For instance, their narrow extent in frequency space make them very sensitive to Doppler shifts, such that their shape encodes the motion of the medium along the line of sight.
 As a result, given a good model for the line formation process and an inversion method, these physical and chemical properties can be retrieved from observations.
 Currently, we mainly focus on retrieving the distributions of the abundance of the chemical species producing the line, the velocity field, and its kinetic temperature.
 However, also other parameters can be retrieved.
 
-More information about the model for [spectral line formation](https://p3droslo.readthedocs.io/en/latest/background/spectral_line_formation.html) and the [probabilistic reconstruction methods](https://p3droslo.readthedocs.io/en/latest/background/probabilistic_reconstruction.html) can be found in the [background](https://p3droslo.readthedocs.io/en/latest/background/index.html) pages.
+More information about the model for [spectral line formation](https://pomme.readthedocs.io/en/latest/background/spectral_line_formation.html) and the [probabilistic reconstruction methods](https://pomme.readthedocs.io/en/latest/background/probabilistic_reconstruction.html) can be found in the [background](https://pomme.readthedocs.io/en/latest/background/index.html) pages.
 
-*p3droslo* is built on top of [PyTorch](https://pytorch.org) and benefits a lot from functionality provided by [Astropy](https://www.astropy.org).
+*pomme* is built on top of [PyTorch](https://pytorch.org) and benefits a lot from functionality provided by [Astropy](https://www.astropy.org).
 It is currently developed and maintained by [Frederik De Ceuster](https://freddeceuster.github.io) at [KU Leuven](https://www.kuleuven.be/english/kuleuven/index.html).
 
 
 ## Installation
 
-Get the latest release (version 0.0.15) either from [PyPI](https://pypi.org/project/p3droslo/), using `pip`, with:
+Get the latest release (version 0.0.15) either from [PyPI](https://pypi.org/project/pomme/), using `pip`, with:
 ```
-pip install p3droslo
+pip install pomme
 ```
-or from [Anaconda.org](https://anaconda.org/FredDeCeuster/p3droslo), using `conda`, with:
+or from [Anaconda.org](https://anaconda.org/FredDeCeuster/pomme), using `conda`, with:
 ```
-conda install -c freddeceuster p3droslo 
+conda install -c freddeceuster pomme 
 ```
-or download the [source code](https://github.com/Magritte-code/p3droslo/archive/refs/heads/main.zip), unzip, and install with `pip` by executing:
+or download the [source code](https://github.com/Magritte-code/pomme/archive/refs/heads/main.zip), unzip, and install with `pip` by executing:
 ```
 pip install .
 ```
@@ -43,17 +43,17 @@ in the root directory of the code.
 
 ## Documentation
 
-Documentation with examples can be found at [p3droslo.readthedocs.io](https://p3droslo.readthedocs.io/en/latest/).
+Documentation with examples can be found at [pomme.readthedocs.io](https://pomme.readthedocs.io/en/latest/).
 
 
 ## Issues
 
-Please report any issues with this software or its documentation [here](https://github.com/Magritte-code/p3droslo/issues).
+Please report any issues with this software or its documentation [here](https://github.com/Magritte-code/pomme/issues).
 
 
 ## Contributing
 
-We are open to contributions to p3droslo. More information can be found [here](https://github.com/Magritte-code/p3droslo/blob/main/CONTRIBUTING.md).
+We are open to contributions to pomme. More information can be found [here](https://github.com/Magritte-code/pomme/blob/main/CONTRIBUTING.md).
 
 
 ## Collaborating

conda/meta.yaml

@@ -1,9 +1,9 @@
 package:
-  name: p3droslo
+  name: pomme
   version: "0.0.15"
 
 about:
-  home: "https://github.com/Magritte-code/p3droslo"
+  home: "https://github.com/Magritte-code/pomme"
   license: GPLv3
   license_file: LICENSE
   summary: Probabilistic 3D Reconstruction of Spectral Line Observations.

docs/src/API/index.rst

@@ -4,4 +4,4 @@ Python API
 .. toctree::
    :maxdepth: 3
 
-   p3droslo
+   pomme

docs/src/API/p3droslo.forward.rst

@@ -1,7 +1,7 @@
-p3droslo.forward
+pomme.forward
 ================
 
-.. automodule:: p3droslo.forward
+.. automodule:: pomme.forward
    :members:
    :undoc-members:
    :show-inheritance:

docs/src/API/p3droslo.haar.rst

@@ -1,7 +1,7 @@
-p3droslo.haar
+pomme.haar
 =============
 
-.. automodule:: p3droslo.haar
+.. automodule:: pomme.haar
    :members:
    :undoc-members:
    :show-inheritance:

docs/src/API/p3droslo.lines.rst

@@ -1,7 +1,7 @@
-p3droslo.lines
+pomme.lines
 ==============
 
-.. automodule:: p3droslo.lines
+.. automodule:: pomme.lines
    :members:
    :undoc-members:
    :show-inheritance:

docs/src/API/p3droslo.loss.rst

@@ -1,7 +1,7 @@
-p3droslo.loss
+pomme.loss
 =============
 
-.. automodule:: p3droslo.loss
+.. automodule:: pomme.loss
    :members:
    :undoc-members:
    :show-inheritance:

docs/src/API/p3droslo.model.rst

@@ -1,7 +1,7 @@
-p3droslo.model
+pomme.model
 ==============
 
-.. automodule:: p3droslo.model
+.. automodule:: pomme.model
    :members:
    :undoc-members:
    :show-inheritance:

docs/src/API/p3droslo.object.rst

@@ -1,7 +1,7 @@
-p3droslo.object
+pomme.object
 ===============
 
-.. automodule:: p3droslo.object
+.. automodule:: pomme.object
    :members:
    :undoc-members:
    :show-inheritance:

docs/src/API/p3droslo.observation.rst

@@ -1,7 +1,7 @@
-p3droslo.observation
+pomme.observation
 ====================
 
-.. automodule:: p3droslo.observation
+.. automodule:: pomme.observation
    :members:
    :undoc-members:
    :show-inheritance:

docs/src/API/p3droslo.plot.rst

@@ -1,7 +1,7 @@
-p3droslo.plot
+pomme.plot
 =============
 
-.. automodule:: p3droslo.plot
+.. automodule:: pomme.plot
    :members:
    :undoc-members:
    :show-inheritance:

docs/src/API/p3droslo.reconstruction.rst

@@ -1,7 +1,7 @@
-p3droslo.reconstruction
+pomme.reconstruction
 =======================
 
-.. automodule:: p3droslo.reconstruction
+.. automodule:: pomme.reconstruction
    :members:
    :undoc-members:
    :show-inheritance:

docs/src/API/p3droslo.rst

@@ -1,7 +1,7 @@
-p3droslo
+pomme
 ========
 
-.. automodule:: p3droslo
+.. automodule:: pomme
    :members:
    :undoc-members:
    :show-inheritance:
@@ -13,13 +13,13 @@ Submodules
 .. toctree::
    :maxdepth: 0
 
-   p3droslo.forward
-   p3droslo.haar
-   p3droslo.lines
-   p3droslo.loss
-   p3droslo.model
-   p3droslo.object
-   p3droslo.observation
-   p3droslo.plot
-   p3droslo.reconstruction
-   p3droslo.utils
+   pomme.forward
+   pomme.haar
+   pomme.lines
+   pomme.loss
+   pomme.model
+   pomme.object
+   pomme.observation
+   pomme.plot
+   pomme.reconstruction
+   pomme.utils

docs/src/API/p3droslo.utils.rst

@@ -1,7 +1,7 @@
-p3droslo.utils module
+pomme.utils module
 =====================
 
-.. automodule:: p3droslo.utils
+.. automodule:: pomme.utils
    :members:
    :undoc-members:
    :show-inheritance:

docs/src/background/spectral_line_formation.ipynb

@@ -70,7 +70,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The implementation on this line optical depth can be found in [src/p3droslo/lines.py](https://github.com/Magritte-code/p3droslo/blob/main/src/p3droslo/lines.py). It turned out that the implementation with two masks (one for case $\\left|b_{1}-b_{0}\\right| < 10^{-3}$ and one for its complement) is more expensive than doing both calculations for both cases, and only in the end mergingg the result. This, however, will mean that at seem point some $\\Delta \\tau$ will be NaN due to division by zero (coming from $b_{1}-b_{0}$), which causes no problem for the forward model (since these values will eventually be overwritten), but which causes gradients to diverge (see [this issue](https://github.com/Magritte-code/p3droslo/issues/2)). Therefore we add a small number $10^{-30}$ to the denominator."
+    "The implementation on this line optical depth can be found in [src/pomme/lines.py](https://github.com/Magritte-code/pomme/blob/main/src/pomme/lines.py). It turned out that the implementation with two masks (one for case $\\left|b_{1}-b_{0}\\right| < 10^{-3}$ and one for its complement) is more expensive than doing both calculations for both cases, and only in the end mergingg the result. This, however, will mean that at seem point some $\\Delta \\tau$ will be NaN due to division by zero (coming from $b_{1}-b_{0}$), which causes no problem for the forward model (since these values will eventually be overwritten), but which causes gradients to diverge (see [this issue](https://github.com/Magritte-code/pomme/issues/2)). Therefore we add a small number $10^{-30}$ to the denominator."
    ]
   },
   {
@@ -120,7 +120,7 @@
    "metadata": {},
    "source": [
     "in which you can recognize the expansion of the exponential minus the first two terms.\n",
-    "The implementation of this intensity increment can be found in [src/p3droslo/forward.py](https://github.com/Magritte-code/p3droslo/blob/main/src/p3droslo/forward.py). For the same reaseon as with the line optical depth, we compute both cases for all values, to minimise the use of masks, and we add a small number ($10^{-30}$) to the denominator to avoid NaNs in gradients."
+    "The implementation of this intensity increment can be found in [src/pomme/forward.py](https://github.com/Magritte-code/pomme/blob/main/src/pomme/forward.py). For the same reaseon as with the line optical depth, we compute both cases for all values, to minimise the use of masks, and we add a small number ($10^{-30}$) to the denominator to avoid NaNs in gradients."
    ]
   },
   {

docs/src/benchmarks/Benchmark_0.ipynb

@@ -24,8 +24,8 @@
     "import numpy             as np\n",
     "import torch\n",
     "\n",
-    "from p3droslo.model import TensorModel\n",
-    "from p3droslo.lines import Line\n",
+    "from pomme.model import TensorModel\n",
+    "from pomme.lines import Line\n",
     "from astropy        import constants\n",
     "from time           import time\n",
     "from ipywidgets     import interact"

docs/src/benchmarks/Benchmark_1.ipynb

@@ -34,9 +34,9 @@
     "import numpy             as np\n",
     "import torch\n",
     "\n",
-    "from p3droslo.model import TensorModel\n",
-    "from p3droslo.lines import Line\n",
-    "from p3droslo.utils import planck"
+    "from pomme.model import TensorModel\n",
+    "from pomme.lines import Line\n",
+    "from pomme.utils import planck"
    ]
   },
   {