plaseval-report 0.1.0__tar.gz

plaseval_report-0.1.0/LICENSE

@@ -0,0 +1,9 @@
+# MIT License
+
+Copyright 2026 Victor Epain
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

plaseval_report-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: plaseval-report
+Version: 0.1.0
+Summary: Generate figures from PlasEval evaluations
+Author: vepain
+Author-email: vepain <victorepain@disroot.org>
+License: # MIT License
+         
+         Copyright 2026 Victor Epain
+         
+         Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+         
+         The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+         
+         THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+Requires-Dist: loguru>=0.7.3
+Requires-Dist: matplotlib>=3.10.8
+Requires-Dist: pandas[output-formatting]<4.0
+Requires-Dist: pydantic>=2.13.4
+Requires-Dist: pyyaml>=6.0.3
+Requires-Dist: rich>=13.0,<16.0
+Requires-Dist: seaborn<1.0
+Requires-Dist: statannotations>=0.7.2
+Requires-Dist: typer>=0.21.1,<1.0
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown
+
+# Report PlasEval evaluations
+
+[![PyPI][pypi_badge]][pypi_link]
+[![ty][ty_badge]][ty_link]
+[![Ruff][ruff_badge]][ruff_link]
+[![uv][uv_badge]][uv_link]
+[![Pipeline status][pipeline_badge]][pipeline_link]
+[![License][license_badge]][licence_link]
+
+## Installation
+
+```sh
+git clone
+```
+
+### With uv (recommended)
+
+See also [uv](https://docs.astral.sh/uv/).
+
+```sh
+uv sync
+# For Bash:
+source .venv/bin/activate
+# For Fish:
+source .venv/bin/activate.fish
+```
+
+### With virtualenv
+
+```bash
+python3.13 -m virtualenv .venv
+source .venv/bin/activate
+python3.13 -m pip install .
+```
+
+## Usage
+
+In a test directory:
+
+```bash
+tests_dir=tests
+
+mkdir $tests_dir
+```
+
+The next section is about [PlasEval] `comp` command.
+For [PlasEval] `eval` command, the processes are the same.
+
+For more details, use `--help` option:
+
+```bash
+plaseval-report --help
+# or with uv
+uv run plaseval-report --help
+```
+
+### Input data
+
+The main file is a TSV file with the following base content (independent of `comp` or `eval` commands):
+
+| Column ID     | Type  | Description  |
+| ------------- | ----- | ------------ |
+| `species_id`  | `str` | Species code |
+| `sample_uid`  | `str` | Sample UID   |
+| `method_code` | `str` | Method code  |
+
+The following columns are specific to `comp` command:
+
+| Column ID       | Type    | Description          | Measure code |
+| --------------- | ------- | -------------------- | ------------ |
+| `Cuts`          | `float` | Normalized cut cost  | `cuts`       |
+| `Joins`         | `float` | Normalized join cost | `joins`      |
+| `Extra_ctgs`    | `float` | Extra contigs cost   | `extra`      |
+| `Missing_ctgs`  | `float` | Missing contigs cost | `miss`       |
+| `Dissimilarity` | `float` | Dissimilarity        | `diss`       |
+
+The following columns are specific to `eval` command:
+
+| Column ID       | Type    | Description          | Measure code |
+| --------------- | ------- | -------------------- | ------------ |
+| `unw_precision` | `float` | Unweighted precision | `unw_prec`   |
+| `unw_recall`    | `float` | Unweighted recall    | `unw_recall` |
+| `unw_f1`        | `float` | Unweighted F1        | `unw_f1`     |
+| `w_precision`   | `float` | Weighted precision   | `w_prec`     |
+| `w_recall`      | `float` | Weighted recall      | `w_recall`   |
+| `w_f1`          | `float` | Weighted F1          | `w_f1`       |
+
+The configuration of the figures/stats is detailed in the `config.yaml` file (optional):
+
+```yaml
+#
+# (Optional) Method codes options
+#
+methods:
+  #
+  # (Optional) List of method codes to consider.
+  # If not set, all the method codes are considered, and the order is given by the TSV file.
+  # If the key to_show is not set, the method order is given by the `methods` list.
+  #
+  to_consider:
+    - <method_code>
+    - ...
+  #
+  # (Optional) List of method codes to show among the ones in `to_consider`.
+  # If the key to_show is set, the method order is given by the `to_show` list.
+  #
+  to_show:
+    - <method_code>
+    - ...
+  #
+  # (Optional) Map method code to labels
+  #
+  labels:
+    #
+    # One line labels.
+    # If not set, take the wrap labels otherwise the method codes.
+    #
+    one_line:
+      <method_code>: <str>
+      ...
+    #
+    # Labels potentially on several lines.
+    # If not set, take the one_line labels otherwise the method codes.
+    #
+    wrap:
+      <method_code>: <str>
+      ...
+  #
+  # (Optional) List of pairs of methods to annotate with stats
+  #
+  statannotate:
+    - - <method_code>
+      - <method_code>
+    - ...
+  #
+  # Method figure aesthetics
+  #
+  fig_aes:
+    palette: <str> # default: Set3, see https://matplotlib.org/stable/users/explain/colors/colormaps.html#qualitative
+    #
+    # Map method to palette index
+    # By default follow the order of the methods to show.
+    # If one method is missing in the map, automatically set the index to unused ones, then cycle.
+    #
+    color_indices:
+      <method_code>: <int> # The index of the color in the palette
+      ...
+#
+# (Optional) Species options
+# It follows the same structure as for `methods`
+#
+species:
+  ...
+
+#
+# (Optional) Measures options
+#
+measures:
+  #
+  # (Optional) List of measures to consider.
+  # If not set, all the measures are considered, and the order is given by the TSV file.
+  #
+  to_consider:
+    - <measure_code>
+    - ...
+  #
+  # (Optional) List of measures to show among the ones in `to_consider`.
+  #
+  to_show:
+    - <measure_code>
+    - ...
+#
+# (Optional) Samples removal strategy (for the methods listed in `methods`).
+# The option is valid for al but result-presence figures and stats.
+#
+remove_samples: fails | nothing # default: fails
+#
+# Figure aesthetics (Optional, everything is optional)
+#
+fig_aes:
+  context: notebook | paper | talk | poster # default: notebook
+  focus: true | false                       # default: false
+```
+
+### PlasEval comp/eval command results
+
+In what follow, the same subcommands are available for both `comp` and `eval` commands.
+The only difference is in the name of the measures (specific to `comp` and `eval`).
+In what follow, we focus on the `comp` command.
+
+The next section illustrates how to generate the figures.
+Generating the statistics tables is following the same process.
+
+```bash
+plaseval-report comp fig --help
+```
+
+In the next sections, we must tell which methods we want to consider.
+
+#### Result presence figures
+
+Know for each tool how many samples have been evaluated by [PlasEval]:
+
+```bash
+plaseval-report comp fig res-presence "$merge_evals_tsv" "$figs_dir/res-presence" --config "$config_yaml"
+```
+
+#### Distribution figures
+
+```bash
+plaseval-report comp fig distribution "$merge_evals_tsv" "$figs_dir/distribution" --config "$config_yaml"
+```
+
+#### Versus figures
+
+Generate a versus figure:
+
+```bash
+x_axis="pbhmf_rfpl"
+y_axis="gpcc_rfpl"
+
+plaseval-report comp fig versus "$merge_evals_tsv" "$figs_dir/versus" "$x_axis" "$y_axis" --config "$config_yaml"
+```
+
+> [!NOTE]
+> Keys `to_show` are ignored in the versus figure.
+
+<!--  -->
+
+> [!TIP]
+> If you are not setting the option `remove_samples` to `fails`, you can simply list the two methods of the axes in the `to_consider` key.
+
+#### Repeat stats figures
+
+The above figures use an additional TSV file, `repeat_stats.tsv`:
+
+| Column ID      | Description  |
+| -------------- | ------------ |
+| `sample_uid`   | Sample ID    |
+| `species_id`   | Species ID   |
+| `repeat_ratio` | Repeat ratio |
+
+An overview:
+
+```bash
+plaseval-report fig repeat-stats overview "$repeat_stats_tsv" "$figs_dir/repeat-stats/overview" --config "$config_yaml"
+```
+
+Evaluation measures according to the repeat ratio:
+
+```bash
+plaseval-report fig repeat-stats eval "$merge_evals_tsv" "$repeat_stats_tsv" "$figs_dir/repeat_stats/eval" --config "$config_yaml"
+```
+
+### Joining the PlasEval comp and eval evaluations
+
+In order to have the `comp` and `eval` figures on the same samples, we can join the two `TSV` files:
+
+```bash
+plaseval-report utils join-measures --help
+
+join_tsv=comp_eval_merge_evals.tsv
+plaseval-report utils join-measures "$merge_comp_tsv" "$merge_eval_tsv" "$join_tsv"
+```
+
+Joining the two set of measures is relevant when `remove_samples` option is set to `fails` because filtering on the joined TSV ensures all the samples have a `comp` and a `eval` evaluation.
+
+<!-- Links -->
+[PlasEval]: https://github.com/cchauve/PlasEval
+
+<!-- Badges -->
+
+<!--
+Changes:
+
+* PyPI project name `plaseval-report`
+* Git project name `https://gitlab.com/vepain/plaseval_report-py`
+* GitLab project ID `85477466`
+* shields.io GitLab `vepain%2Fplaseval_report-py`
+-->
+
+[pypi_badge]: https://img.shields.io/pypi/v/plaseval-report?style=for-the-badge&logo=python&color=blue "Package badge"
+[pypi_link]: https://pypi.org/project/plaseval-report/ "Package link"
+
+[ruff_badge]: https://img.shields.io/endpoint?url=https%3A%2F%2Fgitlab.com%2Fapi%2Fv4%2Fprojects%2F85477466%2Fjobs%2Fartifacts%2Fmain%2Fraw%2Fruff%2Fbadge.json%3Fjob%3Druff&style=for-the-badge&logo=ruff&label=Ruff "Ruff badge"
+[ruff_link]: https://gitlab.com/vepain/plaseval_report-py/-/commits/main "Ruff link"
+
+<!-- https://gitlab.com/api/v4/projects/85477466/jobs/artifacts/main/raw/ruff/badge.json?job=ruff -->
+
+[ty_badge]: https://img.shields.io/endpoint?url=https%3A%2F%2Fgitlab.com%2Fapi%2Fv4%2Fprojects%2F85477466%2Fjobs%2Fartifacts%2Fmain%2Fraw%2Fty%2Fbadge.json%3Fjob%3Dty&style=for-the-badge&logo=ty&label=Ty "ty badge"
+[ty_link]: https://gitlab.com/vepain/plaseval_report-py/-/commits/main "ty link"
+
+[uv_badge]: https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2Fastral-sh%2Fuv%2Fmain%2Fassets%2Fbadge%2Fv0.json&style=for-the-badge "uv badge"
+[uv_link]: https://docs.astral.sh/uv/ "uv link"
+
+[pipeline_badge]: https://img.shields.io/gitlab/pipeline-status/vepain%2Fplaseval_report-py?branch=main&style=for-the-badge&logo=circleci "Pipeline badge"
+[pipeline_link]: https://gitlab.com/vepain/plaseval_report-py/-/commits/main "Pipeline link"
+
+[license_badge]: https://img.shields.io/gitlab/license/vepain%2Fplaseval_report-py?style=for-the-badge&logo=readdotcv&color=green "Licence badge"
+[licence_link]: https://gitlab.com/vepain/plaseval_report-py "Licence link"

plaseval_report-0.1.0/README.md

@@ -0,0 +1,300 @@
+# Report PlasEval evaluations
+
+[![PyPI][pypi_badge]][pypi_link]
+[![ty][ty_badge]][ty_link]
+[![Ruff][ruff_badge]][ruff_link]
+[![uv][uv_badge]][uv_link]
+[![Pipeline status][pipeline_badge]][pipeline_link]
+[![License][license_badge]][licence_link]
+
+## Installation
+
+```sh
+git clone
+```
+
+### With uv (recommended)
+
+See also [uv](https://docs.astral.sh/uv/).
+
+```sh
+uv sync
+# For Bash:
+source .venv/bin/activate
+# For Fish:
+source .venv/bin/activate.fish
+```
+
+### With virtualenv
+
+```bash
+python3.13 -m virtualenv .venv
+source .venv/bin/activate
+python3.13 -m pip install .
+```
+
+## Usage
+
+In a test directory:
+
+```bash
+tests_dir=tests
+
+mkdir $tests_dir
+```
+
+The next section is about [PlasEval] `comp` command.
+For [PlasEval] `eval` command, the processes are the same.
+
+For more details, use `--help` option:
+
+```bash
+plaseval-report --help
+# or with uv
+uv run plaseval-report --help
+```
+
+### Input data
+
+The main file is a TSV file with the following base content (independent of `comp` or `eval` commands):
+
+| Column ID     | Type  | Description  |
+| ------------- | ----- | ------------ |
+| `species_id`  | `str` | Species code |
+| `sample_uid`  | `str` | Sample UID   |
+| `method_code` | `str` | Method code  |
+
+The following columns are specific to `comp` command:
+
+| Column ID       | Type    | Description          | Measure code |
+| --------------- | ------- | -------------------- | ------------ |
+| `Cuts`          | `float` | Normalized cut cost  | `cuts`       |
+| `Joins`         | `float` | Normalized join cost | `joins`      |
+| `Extra_ctgs`    | `float` | Extra contigs cost   | `extra`      |
+| `Missing_ctgs`  | `float` | Missing contigs cost | `miss`       |
+| `Dissimilarity` | `float` | Dissimilarity        | `diss`       |
+
+The following columns are specific to `eval` command:
+
+| Column ID       | Type    | Description          | Measure code |
+| --------------- | ------- | -------------------- | ------------ |
+| `unw_precision` | `float` | Unweighted precision | `unw_prec`   |
+| `unw_recall`    | `float` | Unweighted recall    | `unw_recall` |
+| `unw_f1`        | `float` | Unweighted F1        | `unw_f1`     |
+| `w_precision`   | `float` | Weighted precision   | `w_prec`     |
+| `w_recall`      | `float` | Weighted recall      | `w_recall`   |
+| `w_f1`          | `float` | Weighted F1          | `w_f1`       |
+
+The configuration of the figures/stats is detailed in the `config.yaml` file (optional):
+
+```yaml
+#
+# (Optional) Method codes options
+#
+methods:
+  #
+  # (Optional) List of method codes to consider.
+  # If not set, all the method codes are considered, and the order is given by the TSV file.
+  # If the key to_show is not set, the method order is given by the `methods` list.
+  #
+  to_consider:
+    - <method_code>
+    - ...
+  #
+  # (Optional) List of method codes to show among the ones in `to_consider`.
+  # If the key to_show is set, the method order is given by the `to_show` list.
+  #
+  to_show:
+    - <method_code>
+    - ...
+  #
+  # (Optional) Map method code to labels
+  #
+  labels:
+    #
+    # One line labels.
+    # If not set, take the wrap labels otherwise the method codes.
+    #
+    one_line:
+      <method_code>: <str>
+      ...
+    #
+    # Labels potentially on several lines.
+    # If not set, take the one_line labels otherwise the method codes.
+    #
+    wrap:
+      <method_code>: <str>
+      ...
+  #
+  # (Optional) List of pairs of methods to annotate with stats
+  #
+  statannotate:
+    - - <method_code>
+      - <method_code>
+    - ...
+  #
+  # Method figure aesthetics
+  #
+  fig_aes:
+    palette: <str> # default: Set3, see https://matplotlib.org/stable/users/explain/colors/colormaps.html#qualitative
+    #
+    # Map method to palette index
+    # By default follow the order of the methods to show.
+    # If one method is missing in the map, automatically set the index to unused ones, then cycle.
+    #
+    color_indices:
+      <method_code>: <int> # The index of the color in the palette
+      ...
+#
+# (Optional) Species options
+# It follows the same structure as for `methods`
+#
+species:
+  ...
+
+#
+# (Optional) Measures options
+#
+measures:
+  #
+  # (Optional) List of measures to consider.
+  # If not set, all the measures are considered, and the order is given by the TSV file.
+  #
+  to_consider:
+    - <measure_code>
+    - ...
+  #
+  # (Optional) List of measures to show among the ones in `to_consider`.
+  #
+  to_show:
+    - <measure_code>
+    - ...
+#
+# (Optional) Samples removal strategy (for the methods listed in `methods`).
+# The option is valid for al but result-presence figures and stats.
+#
+remove_samples: fails | nothing # default: fails
+#
+# Figure aesthetics (Optional, everything is optional)
+#
+fig_aes:
+  context: notebook | paper | talk | poster # default: notebook
+  focus: true | false                       # default: false
+```
+
+### PlasEval comp/eval command results
+
+In what follow, the same subcommands are available for both `comp` and `eval` commands.
+The only difference is in the name of the measures (specific to `comp` and `eval`).
+In what follow, we focus on the `comp` command.
+
+The next section illustrates how to generate the figures.
+Generating the statistics tables is following the same process.
+
+```bash
+plaseval-report comp fig --help
+```
+
+In the next sections, we must tell which methods we want to consider.
+
+#### Result presence figures
+
+Know for each tool how many samples have been evaluated by [PlasEval]:
+
+```bash
+plaseval-report comp fig res-presence "$merge_evals_tsv" "$figs_dir/res-presence" --config "$config_yaml"
+```
+
+#### Distribution figures
+
+```bash
+plaseval-report comp fig distribution "$merge_evals_tsv" "$figs_dir/distribution" --config "$config_yaml"
+```
+
+#### Versus figures
+
+Generate a versus figure:
+
+```bash
+x_axis="pbhmf_rfpl"
+y_axis="gpcc_rfpl"
+
+plaseval-report comp fig versus "$merge_evals_tsv" "$figs_dir/versus" "$x_axis" "$y_axis" --config "$config_yaml"
+```
+
+> [!NOTE]
+> Keys `to_show` are ignored in the versus figure.
+
+<!--  -->
+
+> [!TIP]
+> If you are not setting the option `remove_samples` to `fails`, you can simply list the two methods of the axes in the `to_consider` key.
+
+#### Repeat stats figures
+
+The above figures use an additional TSV file, `repeat_stats.tsv`:
+
+| Column ID      | Description  |
+| -------------- | ------------ |
+| `sample_uid`   | Sample ID    |
+| `species_id`   | Species ID   |
+| `repeat_ratio` | Repeat ratio |
+
+An overview:
+
+```bash
+plaseval-report fig repeat-stats overview "$repeat_stats_tsv" "$figs_dir/repeat-stats/overview" --config "$config_yaml"
+```
+
+Evaluation measures according to the repeat ratio:
+
+```bash
+plaseval-report fig repeat-stats eval "$merge_evals_tsv" "$repeat_stats_tsv" "$figs_dir/repeat_stats/eval" --config "$config_yaml"
+```
+
+### Joining the PlasEval comp and eval evaluations
+
+In order to have the `comp` and `eval` figures on the same samples, we can join the two `TSV` files:
+
+```bash
+plaseval-report utils join-measures --help
+
+join_tsv=comp_eval_merge_evals.tsv
+plaseval-report utils join-measures "$merge_comp_tsv" "$merge_eval_tsv" "$join_tsv"
+```
+
+Joining the two set of measures is relevant when `remove_samples` option is set to `fails` because filtering on the joined TSV ensures all the samples have a `comp` and a `eval` evaluation.
+
+<!-- Links -->
+[PlasEval]: https://github.com/cchauve/PlasEval
+
+<!-- Badges -->
+
+<!--
+Changes:
+
+* PyPI project name `plaseval-report`
+* Git project name `https://gitlab.com/vepain/plaseval_report-py`
+* GitLab project ID `85477466`
+* shields.io GitLab `vepain%2Fplaseval_report-py`
+-->
+
+[pypi_badge]: https://img.shields.io/pypi/v/plaseval-report?style=for-the-badge&logo=python&color=blue "Package badge"
+[pypi_link]: https://pypi.org/project/plaseval-report/ "Package link"
+
+[ruff_badge]: https://img.shields.io/endpoint?url=https%3A%2F%2Fgitlab.com%2Fapi%2Fv4%2Fprojects%2F85477466%2Fjobs%2Fartifacts%2Fmain%2Fraw%2Fruff%2Fbadge.json%3Fjob%3Druff&style=for-the-badge&logo=ruff&label=Ruff "Ruff badge"
+[ruff_link]: https://gitlab.com/vepain/plaseval_report-py/-/commits/main "Ruff link"
+
+<!-- https://gitlab.com/api/v4/projects/85477466/jobs/artifacts/main/raw/ruff/badge.json?job=ruff -->
+
+[ty_badge]: https://img.shields.io/endpoint?url=https%3A%2F%2Fgitlab.com%2Fapi%2Fv4%2Fprojects%2F85477466%2Fjobs%2Fartifacts%2Fmain%2Fraw%2Fty%2Fbadge.json%3Fjob%3Dty&style=for-the-badge&logo=ty&label=Ty "ty badge"
+[ty_link]: https://gitlab.com/vepain/plaseval_report-py/-/commits/main "ty link"
+
+[uv_badge]: https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2Fastral-sh%2Fuv%2Fmain%2Fassets%2Fbadge%2Fv0.json&style=for-the-badge "uv badge"
+[uv_link]: https://docs.astral.sh/uv/ "uv link"
+
+[pipeline_badge]: https://img.shields.io/gitlab/pipeline-status/vepain%2Fplaseval_report-py?branch=main&style=for-the-badge&logo=circleci "Pipeline badge"
+[pipeline_link]: https://gitlab.com/vepain/plaseval_report-py/-/commits/main "Pipeline link"
+
+[license_badge]: https://img.shields.io/gitlab/license/vepain%2Fplaseval_report-py?style=for-the-badge&logo=readdotcv&color=green "Licence badge"
+[licence_link]: https://gitlab.com/vepain/plaseval_report-py "Licence link"

plaseval_report-0.1.0/pyproject.toml

@@ -0,0 +1,64 @@
+[project]
+name = "plaseval-report"
+version = "0.1.0"
+description = "Generate figures from PlasEval evaluations"
+readme = "README.md"
+requires-python = ">=3.13"
+dependencies = [
+    "loguru>=0.7.3",
+    "matplotlib>=3.10.8",
+    "pandas[output-formatting]<4.0",
+    "pydantic>=2.13.4",
+    "pyyaml>=6.0.3",
+    "rich>=13.0,<16.0",
+    "seaborn<1.0",
+    "statannotations>=0.7.2",
+    "typer>=0.21.1,<1.0",
+]
+
+[project.license]
+file = "LICENSE"
+
+[[project.authors]]
+name = "vepain"
+email = "victorepain@disroot.org"
+
+[project.scripts]
+plaseval-report = "plaseval_report.__main__:main"
+
+[build-system]
+requires = ["uv_build>=0.12.5,<0.13.0"]
+build-backend = "uv_build"
+
+[dependency-groups]
+dev = [
+    { include-group = "stubs" },
+    "deptry>=0.24.0",
+]
+stubs = [
+    "pandas-stubs>=3.0.0.260204",
+    "types-seaborn>=0.13.2.20251221",
+]
+
+[tool.ruff.lint]
+select = ["ALL"]
+ignore = [
+    "D213",
+    "D203",
+    "TD",
+    "FIX",
+    "CPY001",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.extend-per-file-ignores]
+"tests/**/*.py" = [
+    "S101",
+    "ARG",
+    "FBT",
+    "PLR2004",
+    "S311",
+    "D103",
+]