Fix dependencies

.github/workflows/pytest.yml

@@ -2,25 +2,23 @@ name: pytest
 
 # Controls when the workflow will run
 on: [push, pull_request, workflow_dispatch]
-  # Triggers the workflow on push or pull request events but only for the master branch
+  # Triggers the workflow on push or pull request events for all branches
   # workflow_dispatch allows you to run this workflow manually from the Actions tab
 
 jobs:
   test:
     # The type of runner and python versions that the job will run on
     strategy:
       matrix:
-        os: [windows-latest, ubuntu-20.04, ubuntu-latest]
-        python-version: ["3.11", '3.12', '3.13']
+        os: [windows-latest, ubuntu-latest]
+        python-version: ['3.11', '3.12', '3.13', '3.14']
         full-test:
-          - ${{ contains(github.ref, 'master') || contains(github.ref, 'main') || startsWith(github.ref, 'refs/heads/release') }}
+          - ${{ github.ref == 'refs/heads/developing' || github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/heads/release') }}
         exclude:
           - full-test: false
-            python-version: ["3.10"]
+            python-version: '3.11'
           - full-test: false
-            python-version: ["3.11"]
-          - full-test: false
-            os: "ubuntu-20.04"
+            python-version: '3.12'
       fail-fast: false
     runs-on: ${{ matrix.os }}
 
@@ -108,8 +106,8 @@ jobs:
 
       # Upload coverage to Codecov. Do it only for one case of the matrix.
       - name: Upload coverage to Codecov
-        # do it only once for python 3.12
-        if: matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest'
+        # do it only once for python 3.13 (runs on every branch)
+        if: matrix.python-version == '3.13' && matrix.os == 'ubuntu-latest'
         uses: codecov/codecov-action@v4
         with:
           verbose: true

.readthedocs.yaml

@@ -27,4 +27,7 @@ sphinx:
 # Optionally declare the Python requirements required to build your docs
 python:
   install:
-    - requirements: docs/source/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

AGENTS.md

@@ -4,14 +4,14 @@ JADE is a Python V&V (Verification & Validation) framework for nuclear data libr
 
 - **Documentation**: [ReadTheDocs](https://jade-a-nuclear-data-libraries-vv-tool.readthedocs.io/en/latest/)
 - **PyPI package**: `jadevv` (imports as `jade`)
-- **Python**: ≥ 3.10
+- **Python**: ≥ 3.11
 
 ---
 
 ## Setup
 
 ```bash
-pip install -e .[dev,ui]   # dev tools: pytest, ruff, sphinx; ui: ttkthemes
+pip install -e .[dev,ui,docs]   # dev: pytest, ruff; ui: ttkthemes; docs: sphinx
 ```
 
 ## Running Tests
@@ -59,8 +59,8 @@ Every transport-code-extensible concept uses this pattern:
 
 ```python
 # helper/constants.py
-class CODE(str, Enum):
-    mcnp = "mcnp"; openmc = "openmc"; serpent = "serpent"; d1s = "d1s"; exp = "exp"
+class CODE(Enum):
+    MCNP = "mcnp"; OPENMC = "openmc"; SERPENT = "serpent"; D1S = "d1s"; ACTINV = "actinv"; EXPERIMENT = "exp"
 
 # e.g. run/benchmark.py
 class SingleRun(ABC): ...
@@ -70,7 +70,7 @@ class SingleRunFactory:
     def create(code: CODE, ...) -> SingleRun: ...
 ```
 
-The same pattern applies to `Library`/`LibraryFactory`, `Input`/`InputFactory`, and `AbstractSimOutput`.
+The same pattern applies to `Library`/`LibraryFactory`. `Input` subclasses are selected by `CODE` inside `BenchmarkRun` (`run/benchmark.py`), and `AbstractSimOutput` subclasses inside `RawProcessor.__init__()` (`post/raw_processor.py`).
 
 ### Config construction: always via named classmethods
 
@@ -96,7 +96,7 @@ Expensive state (e.g. `GlobalStatus.simulations`) uses `@property` with an inter
 
 ### `from __future__ import annotations`
 
-Every module starts with this import.
+New modules should start with this import (most existing modules already do).
 
 ---
 
@@ -114,8 +114,8 @@ See [dev guide](docs/source/dev/add_transport_code.rst) for full details. The fo
 
 1. `src/jade/helper/constants.py` — add tag to `CODE` enum
 2. `src/jade/config/run_config.py` — subclass `Library`, register in `LibraryFactory`
-3. `src/jade/run/benchmark.py` + `src/jade/run/input.py` — subclass `SingleRun` (implement `_build_command()`, `_get_lib_data_command()`) and `Input` (implement `set_nps()`, `translate()`, `_write()`); register in `SingleRunFactory`
-4. `src/jade/post/sim_output.py` — subclass `AbstractSimOutput`; wire into `RawProcessor.__init__()`
+3. `src/jade/run/benchmark.py` + `src/jade/run/input.py` — subclass `SingleRun` (implement `_build_command()`, `_get_lib_data_command()`) and `Input` (implement `set_nps()`, `translate()`, `_write()`); register in `SingleRunFactory` and in the input selection of `BenchmarkRun`
+4. `src/jade/post/sim_output.py` — subclass `AbstractSimOutput`; wire into `RawProcessor.__init__()` in `src/jade/post/raw_processor.py`
 
 Add tests mirroring the new code's path under `tests/`.
 
@@ -135,7 +135,7 @@ Input files are hosted externally (not in this repo): IAEA GitHub for open bench
 
 ## Branching & Versioning
 
-- Permanent branches: `master` (stable), `developing` (integration)
+- Permanent branches: `developing` (default, integration), `master` (stable)
 - Branch types: `Feature/*` and `Benchmark/*` off `developing`; `Release/*` for stabilization; `Hotfix/*` off `master`
 - **Semantic versioning**: Major = non-backwards-compatible change (new transport code, class restructure, folder layout). Minor = new features/benchmarks. Patch = bug fixes.
 - Every bug fix must include a regression test.
@@ -145,7 +145,8 @@ Input files are hosted externally (not in this repo): IAEA GitHub for open bench
 
 ## CI Matrix
 
-- **OS**: `ubuntu-latest`, `ubuntu-20.04`, `windows-latest`
-- **Python**: 3.11, 3.12, 3.13
-- Full matrix only on `master`/`release*`; feature branches run latest Python on Ubuntu only.
+- **OS**: `ubuntu-latest`, `windows-latest`
+- **Python**: 3.11, 3.12, 3.13, 3.14
+- Full matrix only on pushes to `developing`/`master`/`release*`; other branches and PRs run only the two latest Python versions (both OSes).
+- Coverage is uploaded to Codecov from the Ubuntu / Python 3.13 job.
 - OpenMC is installed on Linux only; Windows CI skips OpenMC tests.

docs/source/usage/installation.rst

@@ -23,7 +23,7 @@ Or if you are using Anaconda:
   | ``conda activate jade``
 
 .. warning:: 
-  JADE officially supports only Python 3.10, 3.11 and 3.12.
+  JADE officially supports only Python 3.11, 3.12, 3.13 and 3.14.
   It may work with other versions, but they are untested.
 
 Install the JADE package
@@ -74,10 +74,21 @@ You can either dowload the zip file or clone it using git with:
 Moving into the downloaded folder, the user can install the ``jade`` python package
 through a local pip install.
 
-It is recommeded to use the '-e' option when installing (editable mode)
-and you should also install the additional 'dev' dependencies. 
+It is recommended to use the '-e' option when installing (editable mode),
+together with the optional dependency groups needed for development:
 
-  | ``pip install -e .[dev]``
+  | ``pip install -e .[dev,ui,docs]``
+
+The available optional dependency groups are:
+
+- ``dev``: testing and formatting tools (``pytest``, ``pytest-cov``, ``pytest-xvfb``, ``ruff``).
+- ``ui``: GUI dependencies (``ttkthemes``). Skip it on systems without Tkinter.
+- ``docs``: tools needed to build this documentation locally (``sphinx`` and its extensions).
+
+All dependencies are declared in ``pyproject.toml``, which is the single source of truth
+(the documentation build on Read the Docs also installs from it). Most dependencies are capped
+at their current major version (minor version for ``0.x`` packages); when bumping a cap,
+make sure the test suite still passes.
 
 If your dev system allows it, install also openmc in the same python environment.
 

pyproject.toml

@@ -11,38 +11,39 @@ authors = [
 ]
 description = "JADE, a V&V tool for nuclear data libraries and transport codes"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: European Union Public Licence 1.2 (EUPL 1.2)",
     "Operating System :: OS Independent",
 ]
 dependencies = [
-    "xlsxwriter",
-    "matplotlib",
-    "aspose-words",
-    "requests",
-    "f4enix >= 1.0.0",
-    "pyyaml",
-    "seaborn",
-    "python-gitlab"
+    "xlsxwriter < 4",
+    "matplotlib < 4",
+    "requests < 3",
+    "f4enix >= 1.2.1, < 2",
+    "pyyaml < 7",
+    "seaborn < 0.14",
+    "python-gitlab < 9"
 ]
 
 [project.optional-dependencies]
 dev = [
-    "pytest",
-    "pytest-cov",
-    "pytest-xvfb",  # needed for headless display
+    "pytest < 10",
+    "pytest-cov < 8",
+    "pytest-xvfb < 4",  # needed for headless display
     "ruff",  # best formatter that should be used by everybody
-    "sphinx",
-    "myst-parser",
-    "sphinx-book-theme",
-    "sphinx-copybutton",
-    "sphinx-togglebutton",
-    "sphinx-design"
+]
+docs = [
+    "sphinx < 10",
+    "myst-parser < 6",
+    "sphinx-book-theme < 2",
+    "sphinx-copybutton < 0.6",
+    "sphinx-togglebutton < 0.5",
+    "sphinx-design < 0.8"
 ]
 ui = [
-    "ttkthemes"
+    "ttkthemes < 4"
 ]
 
 [project.urls]

src/jade/app/fetch.py

@@ -16,6 +16,7 @@
 
 IAEA_URL = r"https://github.com/IAEA-NDS/open-benchmarks/archive/main.zip"
 RAW_DATA_GITHUB_URL = r"https://github.com/JADE-V-V/JADE-RAW-RESULTS/archive/main.zip"
+GITLAB_TIMEOUT = 30  # seconds
 
 
 def _fetch_from_git(
@@ -90,13 +91,22 @@ def fetch_from_gitlab(
     extracted_folder: Pathlike | bool
         path to the extracted folder. False if the download was not successful.
     """
-    gl = gitlab.Gitlab(url=url, private_token=authorization_token, ssl_verify=False)
+    gl = gitlab.Gitlab(
+        url=url,
+        private_token=authorization_token,
+        ssl_verify=False,
+        timeout=GITLAB_TIMEOUT,
+    )
     try:
         gl.auth()
     except gitlab.exceptions.GitlabAuthenticationError as e:
         logger.error("Gitlab authentication failed")
         logger.error(e)
         return False
+    except requests.exceptions.RequestException as e:
+        logger.error(f"Could not connect to {url}")
+        logger.error(e)
+        return False
 
     # select the correct project
     found = False
@@ -125,6 +135,7 @@ def _install_data(fetch_folder: str | os.PathLike, install_folder: str | os.Path
             os.path.join(install_folder, item),
         )
 
+
 def _install_standard_folder_structure(
     extracted_folder: str | os.PathLike,
     inputs_root: PathLike,

src/jade/post/excel_routines.py

@@ -180,7 +180,7 @@ def _rename_columns(df: pd.DataFrame, names: dict[str, str]) -> None:
             col_names = {k: v for k, v in names.items() if k in df.columns.names}
             df.columns = df.columns.rename(col_names)
         else:
-            df.rename(columns=names, inplace=True)
+            df.columns = df.rename(columns=names).columns
 
     @staticmethod
     def _select_common_index_data(
@@ -223,7 +223,7 @@ def _get_sheet(self) -> list[pd.DataFrame]:
         )
         # this is needed to avoid NaN in the multiindex which would cause incorrect dump
         value_df.columns = pd.MultiIndex.from_frame(
-            value_df.columns.to_frame().fillna("")
+            value_df.columns.to_frame().astype(object).fillna("")
         )
 
         if self.cfg.add_error:
@@ -233,7 +233,7 @@ def _get_sheet(self) -> list[pd.DataFrame]:
             # this is needed to avoid NaN in the multiindex which would cause incorrect
             # dump
             ref_err.columns = pd.MultiIndex.from_frame(
-                ref_err.columns.to_frame().fillna("")
+                ref_err.columns.to_frame().astype(object).fillna("")
             )
 
             target_err = self.target_df.pivot(
@@ -242,7 +242,7 @@ def _get_sheet(self) -> list[pd.DataFrame]:
             # this is needed to avoid NaN in the multiindex which would cause incorrect
             # dump
             target_err.columns = pd.MultiIndex.from_frame(
-                target_err.columns.to_frame().fillna("")
+                target_err.columns.to_frame().astype(object).fillna("")
             )
 
             return [value_df, ref_err, target_err]

src/jade/post/manipulate_tally.py

@@ -260,7 +260,7 @@ def groupby(tally: pd.DataFrame, by: str, action: str) -> pd.DataFrame:
         # a series has been created but we want a df
         df = df.to_frame().T
     else:
-        df.reset_index(inplace=True)
+        df = df.reset_index()
 
     return df
 

src/jade/post/plotter.py

@@ -753,9 +753,9 @@ def _get_figure(self) -> tuple[Figure, Axes]:
         if isinstance(axes, Axes):
             axes = [axes]
 
+        data = [(codelib, df.set_index("User")) for codelib, df in self.data]
         indices = []
-        for idx, (codelib, df) in enumerate(self.data):
-            df.set_index("User", inplace=True)
+        for _, df in data:
             indices.extend(df.index.to_list())
 
         # build a common index of isotopes so that the colors are the same for all
@@ -766,7 +766,7 @@ def _get_figure(self) -> tuple[Figure, Axes]:
         for idx, isotope in enumerate(isotopes):
             if int(isotope) == 0:
                 continue
-            for i, (codelib, df) in enumerate(self.data):
+            for i, (_, df) in enumerate(data):
                 if i == 0:
                     _, label = LM.get_zaidname(str(abs(isotope)))
                 else:
@@ -788,7 +788,7 @@ def _get_figure(self) -> tuple[Figure, Axes]:
                     linewidth=0.5,
                 )
 
-        for i, ax in enumerate(axes):
+        for ax, (codelib, _) in zip(axes, data):
             # --- Plot details ---
             # ax details
             ax.set_title(codelib)
@@ -1177,6 +1177,8 @@ def _shorten_x_name(ax: Axes, shorten_x_name: int) -> None:
     for label in ax.get_xticklabels():
         split = label.get_text().split("_")
         new_labels.append(" ".join(split[-shorten_x_name:]))
+    # fix the current ticks so that the new labels stay attached to them
+    ax.set_xticks(ax.get_xticks())
     ax.set_xticklabels(new_labels)