Repository: plantnet/malpolon (language: python)

Issue:
Python3 10 update
# Reference Issues/PRs

This PR ensures support for Python 3.10 as many libraries such as `torchgeo`have dropped their support for Python 3.8 since [NEP29](https://numpy.org/neps/nep-0029-deprecation_policy.html).

This update also comes with improved READMEs instructions and adresses issue #6 .

# What does this implement/fix? Explain your changes.
## Major improvements
- Updated major packages' versions
- Fixed dataloaders to be compatible with new package versions
- Changed functionnal `torchmetrics`calls to match new package version (#6)

## Minor improvements
- Updated trainers config files
- Updated requirements names to offer both Python 3.8 and Python 3.10 requirements options
- Updated github workers config files to use Python 3.10 requirements files by default

# Any other comments?

Accuracy fails on torchmetrics 0.11
The functional torchmetrics.functional.Accuracy requires a third parameter "task" since version 0.11. 

Solution proposition : instantiate the accuracy class on row 137 file standard_prediction_systems.py 
```Accuracy(task="multiclass", num_classes=4)```
drawback : you need to specify the number of classes


Discussion / hints:

Yes, this has come to my attention thanks to Benjamin Bourel and I came to the same conclusion.
Using a class instantiation instead of the functional metric should do the trick but in case of multiclass prediction this indeed means that specifying the number of classes is necessary. 

Furthermore, this problem extends to the user's main script, when specifying the metrics of any class inheriting the `GenericPredictionSystem` class during the instantiation.

But in the case of `standard_prediction_systems.py` since the metric defined there is currently designed to be a fail safe in case no metrics is specified by the user, we cannot simply put a default value. A better solution might be to infer the number of classes directly from the labels given.
It turns out Torchmetrics has been doing a major code refactoring, splitting their Accuracy class and functional metric in all its specific use case (binary, multiclass, multilabel...) in their 0.10.0 update, and again in the 0.11.0 update.

These refactors are, by essence, not backward compatible, so upgrading torchmetrics to its most stable version (as of today : 0.11.0) implies changing every call to torchmetrics (whether functional of class) and inform users to upgrade their package as well.

This is definitely doable, although the most impacted actors will be the users as most of torchmetrics calls are made in main scripts.
Can we discuss that this Thursday ? I won't be available but @Beniofh can manage.

Fix patch:
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index fe3cb79a..b63742ac 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -11,7 +11,7 @@ jobs:
         runs-on: ubuntu-latest
         strategy:
           matrix:
-            python-version: ["3.8"]
+            python-version: ["3.10"]
         permissions:
           pages: write      
           id-token: write   # to verify the deployment originates from an appropriate source
@@ -24,12 +24,13 @@ jobs:
             - uses: actions/setup-python@v4
               name: Setup python ${{ matrix.python-version }}
               with:
+                cache-dependency-path: '**/requirements_python3.10.txt'
                 python-version: ${{ matrix.python-version }}
                 cache: 'pip' # caching pip dependencies
             - name: install cartopy system packages
               run: sudo apt-get install libgeos-dev
-            - name: pip install -r requirements.txt
-              run: pip install -r ./requirements.txt
+            - name: pip install -r requirements_python3.10.txt
+              run: pip install -r ./requirements_python3.10.txt
             - name: pip install -e .
               run: |
                 pip install -e .
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
new file mode 100644
index 00000000..cacde4e1
--- /dev/null
+++ b/CODE_OF_CONDUCT.md
@@ -0,0 +1,133 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+theo.larcher@inria.fr.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 00000000..d8a6fa99
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,19 @@
+# Contributing
+
+## Steps
+
+If you're interested in contributing to the project, please follow these steps:
+1. Fork the repository.
+2. Create a new branch for your feature or bug fix.
+3. Make the necessary changes and commit them.
+4. Open a pull request, referencing the related issue if applicable.
+5. Wait for the project maintainers to review your pull request.
+6. Collaborate and adress any feedback provided.
+
+## Important
+
+In order to ensure the project remains completely free and unencumbered by anyone's copyright monopoly, we ask any major contributors to explicitly dedicate their code-base contributions to the public domain.  
+If possible, the contributors should accompany any non-trivial patches with a simple statement like the following:
+```
+I dedicate any and all copyright interest in this software to the public domain. I make this dedication for the benefit of the public at large and to the detriment of my heirs and successors. I intend this dedication to be an overt act of relinquishment in perpetuity of all present and future rights to this software under copyright law.
+```
\ No newline at end of file
diff --git a/README.md b/README.md
index 7582fd24..11617331 100644
--- a/README.md
+++ b/README.md
@@ -1,18 +1,89 @@
+<p align="center">
+  <a href="https://github.com/plantnet/malpolon/issues"><img src="https://img.shields.io/github/issues/plantnet/malpolon" alt="GitHub issues"></a>
+  <a href="https://github.com/plantnet/malpolon/pulls"><img src="https://img.shields.io/github/issues-pr/plantnet/malpolon" alt="GitHub pull requests"></a>
+  <a href="https://github.com/plantnet/malpolon/graphs/contributors"><img src="https://img.shields.io/github/contributors/plantnet/malpolon" alt="GitHub contributors"></a>
+  <a href="https://github.com/plantnet/malpolon/network/members"><img src="https://img.shields.io/github/forks/plantnet/malpolon" alt="GitHub forks"></a>
+  <a href="https://github.com/plantnet/malpolon/stargazers"><img src="https://img.shields.io/github/stars/plantnet/malpolon" alt="GitHub stars"></a>
+  <a href="https://github.com/plantnet/malpolon/watchers"><img src="https://img.shields.io/github/watchers/plantnet/malpolon" alt="GitHub watchers"></a>
+  <a href="https://github.com/plantnet/malpolon/blob/main/LICENSE"><img src="https://img.shields.io/github/license/plantnet/malpolon" alt="License"></a>
+</p>
+
+<div align="center">
+  <img src="docs/resources/Malpolon_transparent.png" alt="Project logo" width="300">
+  <p align="center">A deep learning framework to help you build your species distribution models</p>
+  <a href="https://github.com/plantnet/malpolon">View framework</a>
+  ·
+  <a href="https://github.com/plantnet/malpolon/issues/new?assignees=aerodynamic-sauce-pan&labels=bug&projects=&template=bug_report.md&title=%5BBUG%5D">Report Bug</a>
+  ·
+  <a href="https://github.com/plantnet/malpolon/issues/new?assignees=aerodynamic-sauce-pan&labels=enhancement&projects=&template=enhancement.md&title=%5BEnhancement%5D">Request Feature</a>
+  <h1></h1>
+</div>
+
 # Malpolon
 
-Malpolon is a framework facilitating the training and sharing of Deep Species Distribution models using various types of input covariates including biodclimatic rasters, remote sensing images, land-use rasters, etc.
+Malpolon is a framework facilitating the training and sharing of Deep Species Distribution models using various types of input covariates including bioclimatic rasters, remote sensing images, land-use rasters, etc...
+
+## Acknowledgments
+
+This work is made possible through public financing by the [European Commission](https://commission.europa.eu/index_en) on european projects [MAMBO](https://www.mambo-project.eu/) and [GUARDEN](https://guarden.org/).
+
+<div align="center">
+  <a href="https://www.mambo-project.eu/"><img src="docs/resources/mambo_logo.png" alt="MAMBO_logo" style="width: 200px;  margin-top: 15px; margin-right: 50px;"></a>
+  <a href="https://guarden.org/"><img src="docs/resources/guarden_logo.png" alt="GUARDEN_logo" style="width: 230px; height: auto; margin-right: 50px;"></a>
+</div>
+<div align="center">
+  <a href="https://commission.europa.eu/index_en"><img src="docs/resources/logo-ec--en.svg" alt="europ_commission_logo" style="width: 300px;  margin-top: 20px; margin-bottom: 15px;"></a>
+</div>
+
+This work is currently under development and maintained by the [Pl@ntNet](https://plantnet.org/) team within the [INRIA](https://www.inria.fr/en) research institute.
+
+<div align="center">
+  <a href="https://www.inria.fr/en"><img src="docs/resources/inria.png" alt="MAMBO_logo" style="width: 150px;  margin-top: 15px; margin-right: 50px;"></a>
+  <a href="https://plantnet.org/"><img src="docs/resources/plantnet_logo.png" alt="GUARDEN_logo" style="width: 250px; height: auto; margin-right: 50px;"></a>
+</div>
+
+## Roadmap
+
+This roadmap outlines the planned features and milestones for the project. Please note that the roadmap is subject to change and may be updated as the project progress.
+
+- [ ] Data support
+    - [x] Images (pre-extracted patches)
+    - [x] Rasters
+    - [ ] Time series
+      - [x] Via GLC23 loaders (.csv)
+      - [ ] Via generic loader
+    - [ ] Shapefiles
+    - [ ] Fuse several data types in one training
+- [ ] Deep learning tasks
+  - [x] Binary classification
+  - [x] Multi-class classification
+  - [x] Multi-label classification
+  - [ ] Regression (abundance prediction)
+  - [ ] Ordinal
+- [ ] Supported models
+  - [x] CNN
+  - [ ] LSTM
+  - [ ] Transformers
+- [ ] Training flexibility
+  - [x] Add model head/tail modifiers
+  - [ ] Allow easy (un-)freeze of layers
+  - [ ] Allow dataset intersections and unions
+- [ ] Allow data parallel training
+  - [x] Multithreading
+  - [ ] Multiprocessing
+    - Issues may arise depending on hardware
 
 ## Installation
 
-To install malpolon, you will first need to install **Python 3.8 or newer**, and several python packages. To do so, it is best practice to create a virtual environment containing all these packages locally.
+To install malpolon, you will first need to install **Python 3.8, 3.9 or 3.10**, and several python packages. To do so, it is best practice to create a virtual environment containing all these packages locally.
 
-⚠️ **macOS** installation may be bumpy for now. More instructions will be added shortly. It is recommended to stick to Linux for the time being. ⚠️
+⚠️ **macOS** installation does not yet include instructions on how to properly set up GPU usage for GPU-enabled mac. For training purposes we recommend sticking to Linux for the time being. ⚠️
 
 ### 0. Requirements
 
 Before proceeding, please make sure the following packages are installed on your system:
 
-- [Python3.8](https://www.python.org/downloads/) (or newer)
+- [3.8 ≤ Python ≤ 3.10](https://www.python.org/downloads/)
 - [`pip`](https://pip.pypa.io/en/stable/installation/)
 - [`git`](https://git-scm.com/downloads)
 - `libgeos-dev` (dependency of Python library `Cartopy`)
@@ -25,6 +96,7 @@ Before proceeding, please make sure the following packages are installed on your
   - [`CUDA Installation guide`](https://docs.nvidia.com/cuda/index.html)
   - [`CuDNN Installation guide`](https://docs.nvidia.com/deeplearning/cudnn/install-guide/index.html)
 
+The following instructions show installation commands for Python 3.10, but can be adapted for any of the compatible Python versions metionned above by simply changing the version number.
 
 ### 1. Clone the repository
 
@@ -37,21 +109,21 @@ git clone https://github.com/plantnet/malpolon.git
 
 ### 2. Create your virtual environment
 
-- **Via `virtualenv` (recommended)**
+- **Via `virtualenv`**
   
 We recommend handling your virtual environment using [`virtualenv`](https://virtualenv.pypa.io/en/stable/) (or similar) and installing the packages via `pip`.
 
 First create your virtual environment using the proper python version, and activate it _(note that in this example, the virtual environment "malpolon_env" will be installed in the current directory)_.
 
 ```script
-virtualenv -p /usr/bin/python3.8 ./malpolon_env
+virtualenv -p /usr/bin/python3.10 ./malpolon_env
 source ./malpolon_env/bin/activate
 ```
 
-Once the env is activated, install the python packages listed in `requirements.txt`:
+Once the env is activated, install the python packages listed in `requirements_python3.10.txt`:
 ```script
 pip install --upgrade setuptools
-pip install -r requirements.txt
+pip install -r requirements_python3.10.txt
 ```
 
 - **Via `conda`**
@@ -97,6 +169,16 @@ The **dev** branch is susceptible to have more up-to-date content such as newer
 git checkout dev
 ```
 
+## Librairies
+Here is an overview of the main Python librairies used in this project. 
+
+* [![PyTorch](https://img.shields.io/badge/PyTorch-%23ee4c2c.svg?logo=pytorch&logoColor=white)](https://pytorch.org/) - To handle deep learning loops and dataloaders
+* [![PyTorch Lightning](https://img.shields.io/badge/PyTorch%20Lightning-%23792EE5.svg?logo=lightning&logoColor=white)](https://lightning.ai/docs/pytorch/stable/) - Deep learning framework which simplifies the usage of PyTorch elements
+* [![Numpy](https://img.shields.io/badge/Numpy-%234D77CF.svg?logo=numpy&logoColor=white)](https://numpy.org/) - For common computational operations
+* [![Torchgeo](https://img.shields.io/badge/Torchgeo-%23EE4C2C.svg?logo=torchgeo&logoColor=white)](https://torchgeo.readthedocs.io/en/stable/) - To handle data rasters
+* [![Matplotlib](https://img.shields.io/badge/Matplotlib-%2311557C.svg?logo=matplotlib&logoColor=white)](https://matplotlib.org/) - For displaying purposes
+* [![Hydra](https://img.shields.io/badge/Hydra-%23729DB1.svg?logo=hydra&logoColor=white)](https://hydra.cc/docs/intro/) - To handle models' hyperparameters
+
 ## Examples
 
 Examples using the GeoLifeCLEF 2022 and 2023 datasets, as well as Sentinel-2A rasters are provided in the `examples` folder. Instructions about how to train and perform predictions with your models can be found in the README file of each example in said folder.
@@ -120,3 +202,6 @@ make -C docs html
 ```
 
 The result can be found in `docs/_build/html`.
+
+## Licensing
+This framework is ditributed under the [MIT license](https://opensource.org/license/mit/), as is the Pl@ntNet project. See LICENSE.md for more information.
diff --git a/SECURITY.md b/SECURITY.md
new file mode 100644
index 00000000..e1b3443f
--- /dev/null
+++ b/SECURITY.md
@@ -0,0 +1,7 @@
+# Security Policy
+
+If you discover a security issue, please bring it to our attention right away!
+
+## Reporting a Vulnerability
+ 
+Please **DO NOT** file a public issue to report a security vulberability, instead send your report privately to **theo.larcher@inria.fr**. This will help ensure that any vulnerabilities that are found can be [disclosed responsibly](https://en.wikipedia.org/wiki/Responsible_disclosure) to any affected parties.
diff --git a/docs/resources/Malpolon_transparent.png b/docs/resources/Malpolon_transparent.png
new file mode 100644
index 00000000..a65d9e6e
Binary files /dev/null and b/docs/resources/Malpolon_transparent.png differ
diff --git a/docs/resources/guarden_logo.png b/docs/resources/guarden_logo.png
new file mode 100644
index 00000000..6e1b48f2
Binary files /dev/null and b/docs/resources/guarden_logo.png differ
diff --git a/docs/resources/inria.png b/docs/resources/inria.png
new file mode 100644
index 00000000..81d24461
Binary files /dev/null and b/docs/resources/inria.png differ
diff --git a/docs/resources/logo-ec--en.svg b/docs/resources/logo-ec--en.svg
new file mode 100644
index 00000000..f864aa1e
--- /dev/null
+++ b/docs/resources/logo-ec--en.svg
@@ -0,0 +1,97 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Generator: Adobe Illustrator 19.2.0, SVG Export Plug-In . SVG Version: 6.00 Build 0)  -->
+<svg version="1.1" id="Layer_1" xmlns:sketch="http://www.bohemiancoding.com/sketch/ns" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px" viewBox="0 0 290 72" style="enable-background:new 0 0 290 72;" xml:space="preserve">
+<style type="text/css">
+.st0 {
+  fill: #bbbdbf;
+}
+.st1 {
+  fill: #034da1;
+}
+.st2 {
+  fill: #fff100;
+}
+.st3 {
+  enable-background: new;
+}
+.st4 {
+  fill: #626366;
+}
+  </style>
+<g>
+	<g id="Page-1" sketch:type="MSPage">
+		<g id="Version-2-menu" transform="translate(-131.000000, -108.000000)" sketch:type="MSArtboardGroup">
+			<g id="Site-header" transform="translate(131.000000, 108.000000)" sketch:type="MSLayerGroup">
+				<g id="logo-copy">
+					<g id="Group-20">
+						<g id="Group-18-Copy" sketch:type="MSShapeGroup">
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+</svg>
\ No newline at end of file
diff --git a/docs/resources/mambo_logo.png b/docs/resources/mambo_logo.png
new file mode 100644
index 00000000..58ec7c0b
Binary files /dev/null and b/docs/resources/mambo_logo.png differ
diff --git a/docs/resources/plantnet_logo.png b/docs/resources/plantnet_logo.png
new file mode 100644
index 00000000..a6e6184d
Binary files /dev/null and b/docs/resources/plantnet_logo.png differ
diff --git a/environment.yml b/environment.yml
index 7f94022f..6e194341 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,5 +7,5 @@ dependencies:
   - cmake==3.26.3
   - pip==23.2.1
   - pip:
-    - -r requirements.txt
+    - -r requirements_python3.10.txt
 prefix: ~/envs/malpolon
diff --git a/examples/geolifeclef2022/cnn_on_rgb_nir_temperature_pedological_patches.py b/examples/geolifeclef2022/cnn_on_rgb_nir_temperature_pedological_patches.py
index e9481a89..7319048d 100644
--- a/examples/geolifeclef2022/cnn_on_rgb_nir_temperature_pedological_patches.py
+++ b/examples/geolifeclef2022/cnn_on_rgb_nir_temperature_pedological_patches.py
@@ -149,8 +149,8 @@ def __init__(
             nesterov=nesterov,
         )
         metrics = {
-            "accuracy": Fmetrics.accuracy,
-            "top_30_accuracy": lambda y_hat, y: Fmetrics.accuracy(y_hat, y, top_k=30),
+            "accuracy": lambda y_hat, y: Fmetrics.classification.multiclass_accuracy(y_hat, y, num_classes=100),
+            "top_30_accuracy": lambda y_hat, y: Fmetrics.classification.multiclass_accuracy(y_hat, y, num_classes=100, top_k=30),
         }
 
         super().__init__(model, loss, optimizer, metrics)
diff --git a/examples/geolifeclef2022/cnn_on_rgb_patches.py b/examples/geolifeclef2022/cnn_on_rgb_patches.py
index f14b9e35..e2a5680a 100644
--- a/examples/geolifeclef2022/cnn_on_rgb_patches.py
+++ b/examples/geolifeclef2022/cnn_on_rgb_patches.py
@@ -93,8 +93,8 @@ def __init__(
         nesterov: bool,
     ):
         metrics = {
-            "accuracy": Fmetrics.accuracy,
-            "top_30_accuracy": lambda y_hat, y: Fmetrics.accuracy(y_hat, y, top_k=30),
+            "accuracy": lambda y_hat, y: Fmetrics.classification.multiclass_accuracy(y_hat, y, num_classes=100),
+            "top_30_accuracy": lambda y_hat, y: Fmetrics.classification.multiclass_accuracy(y_hat, y, num_classes=100, top_k=30),
         }
 
         super().__init__(
@@ -104,6 +104,7 @@ def __init__(
             momentum,
             nesterov,
             metrics,
+            task='multiclass',
         )
 
 
diff --git a/examples/geolifeclef2022/cnn_on_rgb_temperature_patches.py b/examples/geolifeclef2022/cnn_on_rgb_temperature_patches.py
index 5a129880..95b0733f 100644
--- a/examples/geolifeclef2022/cnn_on_rgb_temperature_patches.py
+++ b/examples/geolifeclef2022/cnn_on_rgb_temperature_patches.py
@@ -137,8 +137,8 @@ def __init__(
             nesterov=nesterov,
         )
         metrics = {
-            "accuracy": Fmetrics.accuracy,
-            "top_30_accuracy": lambda y_hat, y: Fmetrics.accuracy(y_hat, y, top_k=30),
+            "accuracy": lambda y_hat, y: Fmetrics.classification.multiclass_accuracy(y_hat, y, num_classes=100),
+            "top_30_accuracy": lambda y_hat, y: Fmetrics.classification.multiclass_accuracy(y_hat, y, num_classes=100, top_k=30),
         }
 
         super().__init__(model, loss, optimizer, metrics)
diff --git a/examples/geolifeclef2022/config/homogeneous_multi_modal_model.yaml b/examples/geolifeclef2022/config/homogeneous_multi_modal_model.yaml
index 9787b177..71592b1a 100644
--- a/examples/geolifeclef2022/config/homogeneous_multi_modal_model.yaml
+++ b/examples/geolifeclef2022/config/homogeneous_multi_modal_model.yaml
@@ -3,7 +3,9 @@ hydra:
     dir: outputs/${hydra.job.name}/${now:%Y-%m-%d_%H-%M-%S}
 
 trainer:
-  gpus: ???
+  # gpus: 1  # Deprecated since pytorchlightning 1.7, removed in 2.0. Replaced by the 2 next attributes
+  accelerator: 'gpu'
+  devices: 1
   max_epochs: 10
   val_check_interval: 0.2
 
diff --git a/examples/geolifeclef2022/config/mono_modal_3_channels_model.yaml b/examples/geolifeclef2022/config/mono_modal_3_channels_model.yaml
index a6f1ddcd..a2addad1 100644
--- a/examples/geolifeclef2022/config/mono_modal_3_channels_model.yaml
+++ b/examples/geolifeclef2022/config/mono_modal_3_channels_model.yaml
@@ -3,7 +3,9 @@ hydra:
     dir: outputs/${hydra.job.name}/${now:%Y-%m-%d_%H-%M-%S}
 
 trainer:
-  gpus: ???
+  # gpus: 1  # Deprecated since pytorchlightning 1.7, removed in 2.0. Replaced by the 2 next attributes
+  accelerator: 'gpu'
+  devices: 1
   max_epochs: 10
   val_check_interval: 0.2
 
diff --git a/examples/geolifeclef2023/example_patch_loading.py b/examples/geolifeclef2023/example_patch_loading.py
index 90d1b46a..44835ec3 100644
--- a/examples/geolifeclef2023/example_patch_loading.py
+++ b/examples/geolifeclef2023/example_patch_loading.py
@@ -13,7 +13,7 @@
 
 def main():
     """Run GLC23 patch example script."""
-    data_path = 'geolifeclef2023/dataset/sample_data/'  # root path of the data
+    data_path = 'dataset/sample_data/'  # root path of the data
 
     # configure providers
     p_rgb = JpegPatchProvider(data_path + 'SatelliteImages/',
diff --git a/examples/geolifeclef2023/example_time_series_loading.py b/examples/geolifeclef2023/example_time_series_loading.py
index 2a27e632..0d03786c 100644
--- a/examples/geolifeclef2023/example_time_series_loading.py
+++ b/examples/geolifeclef2023/example_time_series_loading.py
@@ -13,7 +13,7 @@
 
 def main():
     """Run GLC23 time series example script."""
-    data_path = '/home/tlarcher/Documents/Pl@ntNet/git/GLC/data/sample_data/'  # root path of the data
+    data_path = 'dataset/sample_data/'  # root path of the data
     # configure providers
     ts_red = CSVTimeSeriesProvider(data_path + 'SatelliteTimeSeries/time_series_red.csv')
     ts_multi = MultipleCSVTimeSeriesProvider(data_path + 'SatelliteTimeSeries/',
diff --git a/examples/micro_geolifeclef/cnn_on_rgb_nir_patches.py b/examples/micro_geolifeclef/cnn_on_rgb_nir_patches.py
index 018f8f1e..711bf75a 100644
--- a/examples/micro_geolifeclef/cnn_on_rgb_nir_patches.py
+++ b/examples/micro_geolifeclef/cnn_on_rgb_nir_patches.py
@@ -18,7 +18,7 @@
 from malpolon.logging import Summary
 from malpolon.models import FinetuningClassificationSystem
 
-FMETRICS_CALLABLES = {'binary_accuracy': Fmetrics.accuracy,
+FMETRICS_CALLABLES = {'binary_accuracy': Fmetrics.classification.binary_accuracy,
                       'multiclass_accuracy': Fmetrics.classification.multiclass_accuracy,
                       'multilabel_accuracy': Fmetrics.classification.multilabel_accuracy, }
 
diff --git a/examples/micro_geolifeclef/cnn_on_rgb_patches.py b/examples/micro_geolifeclef/cnn_on_rgb_patches.py
index d7fbfbc3..c8a122cd 100644
--- a/examples/micro_geolifeclef/cnn_on_rgb_patches.py
+++ b/examples/micro_geolifeclef/cnn_on_rgb_patches.py
@@ -16,7 +16,7 @@
 from malpolon.logging import Summary
 from malpolon.models import FinetuningClassificationSystem
 
-FMETRICS_CALLABLES = {'binary_accuracy': Fmetrics.accuracy,
+FMETRICS_CALLABLES = {'binary_accuracy': Fmetrics.classification.binary_accuracy,
                       'multiclass_accuracy': Fmetrics.classification.multiclass_accuracy,
                       'multilabel_accuracy': Fmetrics.classification.multilabel_accuracy, }
 
diff --git a/examples/micro_geolifeclef/config/cnn_on_rgb_nir_patches_config.yaml b/examples/micro_geolifeclef/config/cnn_on_rgb_nir_patches_config.yaml
index db16f402..0e570089 100644
--- a/examples/micro_geolifeclef/config/cnn_on_rgb_nir_patches_config.yaml
+++ b/examples/micro_geolifeclef/config/cnn_on_rgb_nir_patches_config.yaml
@@ -3,7 +3,7 @@ defaults:
 
 run:
   predict: false
-  checkpoint_path: "../2023-08-03_18-52-45/checkpoint-epoch=00-step=244-val_multiclass_accuracy=0.0771.ckpt"  # Relative to hydra.run.dir
+  checkpoint_path:  # Relative to hydra.run.dir
 
 model:
   modifiers:
@@ -16,9 +16,6 @@ model:
     change_last_layer:
       num_outputs: 10
 
-trainer:
-  gpus: 1
-
 data:
   dataset_path: "../../../dataset/"  # Relative to hydra.run.dir
   train_batch_size: 32
diff --git a/examples/micro_geolifeclef/config/cnn_on_rgb_patches_config.yaml b/examples/micro_geolifeclef/config/cnn_on_rgb_patches_config.yaml
index 6ff255c2..b08ef66a 100644
--- a/examples/micro_geolifeclef/config/cnn_on_rgb_patches_config.yaml
+++ b/examples/micro_geolifeclef/config/cnn_on_rgb_patches_config.yaml
@@ -12,7 +12,7 @@ trainer:
 
 run:
   predict: false
-  checkpoint_path: "../2023-08-03_18-44-35/checkpoint-epoch=00-step=244-val_multiclass_accuracy=0.0570.ckpt"  # Relative to hydra.run.dir
+  checkpoint_path:  # Relative to hydra.run.dir
 
 model:
   provider_name: "timm"  # choose from ["timm", "torchvision"]
diff --git a/examples/sentinel2_raster_torchgeo/cnn_on_rgbnir_torchgeo.py b/examples/sentinel2_raster_torchgeo/cnn_on_rgbnir_torchgeo.py
index 5463306a..2a83799b 100644
--- a/examples/sentinel2_raster_torchgeo/cnn_on_rgbnir_torchgeo.py
+++ b/examples/sentinel2_raster_torchgeo/cnn_on_rgbnir_torchgeo.py
@@ -31,7 +31,7 @@
 from malpolon.logging import Summary
 from malpolon.models import FinetuningClassificationSystem
 
-FMETRICS_CALLABLES = {'binary_accuracy': Fmetrics.accuracy,
+FMETRICS_CALLABLES = {'binary_accuracy': Fmetrics.classification.binary_accuracy,
                       'multiclass_accuracy': Fmetrics.classification.multiclass_accuracy,
                       'multilabel_accuracy': Fmetrics.classification.multilabel_accuracy, }
 
diff --git a/examples/sentinel2_raster_torchgeo/config/cnn_on_rgbnir_torchgeo_config.yaml b/examples/sentinel2_raster_torchgeo/config/cnn_on_rgbnir_torchgeo_config.yaml
index 9f6010e9..e1d2bb85 100644
--- a/examples/sentinel2_raster_torchgeo/config/cnn_on_rgbnir_torchgeo_config.yaml
+++ b/examples/sentinel2_raster_torchgeo/config/cnn_on_rgbnir_torchgeo_config.yaml
@@ -12,7 +12,7 @@ trainer:
 
 run:
   predict: false
-  checkpoint_path: ""  # Relative to hydra.run.dir
+  checkpoint_path:  # Relative to hydra.run.dir
                                                                                                                                        
 model:
   provider_name: "timm"  # choose from ["timm", "torchvision"]
diff --git a/malpolon/data/datasets/geolifeclef2023.py b/malpolon/data/datasets/geolifeclef2023.py
index 0c344127..85abbac0 100644
--- a/malpolon/data/datasets/geolifeclef2023.py
+++ b/malpolon/data/datasets/geolifeclef2023.py
@@ -408,7 +408,7 @@ def __init__(self,
             # iterate through all the layers
             for i in range(src.count):
                 # replace the NoData values with np.nan
-                self.data = self.data.astype(np.float)
+                self.data = self.data.astype(float)
                 self.data[i] = np.where(self.data[i] == self.nodata_value[i],
                                         np.nan,
                                         self.data[i])
@@ -789,7 +789,7 @@ def plot_ts(self, item):
                 k_provider = 0 if k_provider.shape[0] == 0 else k_provider[-1][0]
 
                 eos_start_ind = np.where(ts_ == self.eos_replace_value[i])[0]
-                eos_start_ind = eos_start_ind[0] if eos_start_ind != [] else ts_.shape[0] - 1
+                eos_start_ind = eos_start_ind[0] if len(eos_start_ind) > 0 else ts_.shape[0] - 1
                 # display the layer on the corresponding subplot
                 axs[i].plot(range(eos_start_ind), ts_[:eos_start_ind],
                             '-.', c='blue', marker='+')
diff --git a/malpolon/data/datasets/torchgeo_datasets.py b/malpolon/data/datasets/torchgeo_datasets.py
index 0e1ea677..ff162a71 100644
--- a/malpolon/data/datasets/torchgeo_datasets.py
+++ b/malpolon/data/datasets/torchgeo_datasets.py
@@ -395,7 +395,7 @@ def __getitem__(
             will be assumed to be the dataset's.
             If dict, must follow : {'lon': lon, 'lat': lat, <'crs': crs>} and
             the coordinates CRS can be specified. If not, it will be assumed
-            taht it is equal to the dataset's.
+            that it is equal to the dataset's.
             In both cases, a BoundingBox is generated to pursue the query.
 
         Returns
diff --git a/malpolon/logging.py b/malpolon/logging.py
index 65862f74..6a513f54 100644
--- a/malpolon/logging.py
+++ b/malpolon/logging.py
@@ -55,7 +55,7 @@ def _log_data_loading_summary(self, data_loader, split: str) -> None:
         logger = self.logger
 
         if split == "Train":
-            dataset = data_loader.dataset.datasets
+            dataset = data_loader.dataset
         else:
             dataset = data_loader.dataset
 
@@ -106,7 +106,7 @@ def on_train_start(self, trainer: pl.Trainer, model: GenericPredictionSystem) ->
         self._log_data_loading_summary(trainer.train_dataloader, "Train")
 
         logger.info("\n## Validation data")
-        self._log_data_loading_summary(trainer.val_dataloaders[0], "Validation")
+        self._log_data_loading_summary(trainer.val_dataloaders, "Validation")
 
         logger.info("\n# Strategy information")
         logger.info(trainer.strategy)
diff --git a/malpolon/models/multi_modal.py b/malpolon/models/multi_modal.py
index 0c42d442..7f395ae6 100644
--- a/malpolon/models/multi_modal.py
+++ b/malpolon/models/multi_modal.py
@@ -4,7 +4,7 @@
 import torch
 from torch import nn
 from pytorch_lightning.strategies import SingleDeviceStrategy, StrategyRegistry
-from pytorch_lightning.utilities.apply_func import move_data_to_device
+from pytorch_lightning.utilities import move_data_to_device
 
 from .utils import check_model
 
diff --git a/malpolon/models/standard_prediction_systems.py b/malpolon/models/standard_prediction_systems.py
index 371697e5..11c67f63 100644
--- a/malpolon/models/standard_prediction_systems.py
+++ b/malpolon/models/standard_prediction_systems.py
@@ -82,7 +82,10 @@ def _step(
         self.log(f"{split}_loss", loss, **log_kwargs)
 
         for metric_name, metric_func in self.metrics.items():
-            score = metric_func['callable'](y_hat, y, **metric_func['kwargs'])
+            if isinstance(metric_func, dict):
+                score = metric_func['callable'](y_hat, y, **metric_func['kwargs'])
+            else:
+                score = metric_func(y_hat, y)
             self.log(f"{split}_{metric_name}", score, **log_kwargs)
 
         return loss
@@ -277,7 +280,7 @@ def __init__(
 
         if metrics is None:
             metrics = {
-                "accuracy": {'callable': Fmetrics.accuracy,
+                "accuracy": {'callable': Fmetrics.binary_accuracy,
                              'kwargs': {}}
             }
 
diff --git a/requirements_python3.10.txt b/requirements_python3.10.txt
new file mode 100644
index 00000000..3437abbf
--- /dev/null
+++ b/requirements_python3.10.txt
@@ -0,0 +1,48 @@
+Cartopy==0.21.1
+cmake==3.26.3
+coverage==7.2.3
+docstring-parser==0.15
+flake8==6.0.0
+geopandas==0.12.1
+hydra-core==1.3.2
+ipykernel==6.18.2
+ipython==8.7.0
+jupyter==1.0.0
+jupyter-server==1.23.3
+jupyterlab==3.5.0
+lightning==2.0.9.post0
+Markdown==3.4.1
+matplotlib==3.8.0
+notebook==6.5.2
+numpy==1.26.0
+odc-geo==0.3.2
+odc-stac==0.3.3
+omegaconf==2.3.0
+opencv-python==4.7.0.72
+pandas==2.1.1
+Pillow==10.0.1
+planetary-computer==0.4.9
+pydocstyle==6.3.0
+pyflakes==3.0.1
+pylint==2.17.1
+pyproj==3.6.1
+pystac==1.6.1
+pystac-client==0.5.1
+pytest==7.2.2
+pytorch-lightning==2.1.0
+PyYAML==6.0.1
+rasterio==1.3.8.post1
+scikit-learn==1.1.3
+scipy==1.11.3
+shapely==2.0.1
+Sphinx==5.3.0
+stack-data==0.6.2
+tensorboard==2.14.1
+tifffile==2022.10.10
+timm==0.9.2
+torch==2.1.0
+torchgeo==0.5.0
+torchmetrics==1.2.0
+torchvision==0.16.0
+tqdm==4.66.1
+yarl==1.9.2
diff --git a/requirements.txt b/requirements_python3.8.txt
similarity index 100%
rename from requirements.txt
rename to requirements_python3.8.txt


Test patch:
diff --git a/.github/workflows/dispatch-test.yml b/.github/workflows/dispatch-test.yml
index 9166cb02..d05e4967 100644
--- a/.github/workflows/dispatch-test.yml
+++ b/.github/workflows/dispatch-test.yml
@@ -8,19 +8,20 @@ jobs:
         runs-on: ubuntu-latest
         strategy:
           matrix:
-            python-version: ["3.8"]
+            python-version: ["3.10"]
 
         steps:
             - uses: actions/checkout@v3
             - uses: actions/setup-python@v4
               name: Setup python ${{ matrix.python-version }}
               with:
+                cache-dependency-path: '**/requirements_python3.10.txt'
                 python-version: ${{ matrix.python-version }}
                 cache: 'pip' # caching pip dependencies
             - name: install cartopy system packages
               run: sudo apt-get install libgeos-dev
-            - name: pip install -r requirements.txt
-              run: pip install -r ./requirements.txt
+            - name: pip install -r requirements_python3.10.txt
+              run: pip install -r ./requirements_python3.10.txt
             - name: pip install -e .
               run: pip install -e .
             - name: Pytest
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 6c3d38f9..85063750 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,19 +13,20 @@ jobs:
         runs-on: ubuntu-latest
         strategy:
           matrix:
-            python-version: ["3.8"]
+            python-version: ["3.10"]
 
         steps:
             - uses: actions/checkout@v3
-            - uses: actions/setup-python@v4
+            - uses: actions/setup-python@v4   
               name: Setup python ${{ matrix.python-version }}
               with:
+                cache-dependency-path: '**/requirements_python3.10.txt'
                 python-version: ${{ matrix.python-version }}
                 cache: 'pip' # caching pip dependencies
             - name: install cartopy system packages
               run: sudo apt-get install libgeos-dev
-            - name: pip install -r requirements.txt
-              run: pip install -r ./requirements.txt
+            - name: pip install -r requirements_python3.10.txt
+              run: pip install -r ./requirements_python3.10.txt
             - name: pip install -e .
               run: pip install -e .
             - name: Pytest