Updates (#105)

* update to numpy2.0 and pandas2.0

* update pre commit hooks

* update to latest python version

* udpate gitignore

* updated version

* style: pre-commit fixes

* ignore some errors in ipynb files

* pdm updates

* added ruff --fix to pre-commit

* new pre-commit fixes

* change non-covered lines to new python version

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ jobs:
   ci:
     strategy:
       matrix:
-        python-version: ["3.8"]
+        python-version: ["3.13"]
         corsika-version: ["77550"]
         os: [ubuntu-latest]
     runs-on: ${{ matrix.os }}

.gitignore

@@ -8,3 +8,4 @@ corsika-*/
 corsika-*.tar.gz
 node_modules/
 .ipynb_checkpoints/
+.venv/

.pre-commit-config.yaml

@@ -6,35 +6,33 @@ exclude: "(admin/config.h|tests/)"
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.12.1
+    rev: 24.10.0
     hooks:
       - id: black
-        language_version: python3.11
       - id: black-jupyter
-        language_version: python3.11
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.16.0" # replace with latest tag on GitHub
+    rev: "1.19.1" # replace with latest tag on GitHub
     hooks:
       - id: blacken-docs
         additional_dependencies:
           - black==22.12.0
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.13.0
     hooks:
       - id: mypy
         args: [--config-file, ./pyproject.toml]
         additional_dependencies: ["types-toml"]
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         exclude: >
@@ -54,6 +52,7 @@ repos:
       - id: prettier
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.9
+    rev: v0.7.4
     hooks:
       - id: ruff
+        args: [--fix]

docs/examples/complete.ipynb

@@ -243,9 +243,9 @@
     "# Let's see what kind of particles we have in the simulation\n",
     "counts = particles[\"pdgid\"].value_counts()\n",
     "counts.index = counts.index.map(\n",
-    "    lambda pid: f\"{Particle.from_pdgid(pid).name} ({pid})\"\n",
-    "    if pid != 0\n",
-    "    else \"unknown (0)\"\n",
+    "    lambda pid: (\n",
+    "        f\"{Particle.from_pdgid(pid).name} ({pid})\" if pid != 0 else \"unknown (0)\"\n",
+    "    )\n",
     ")\n",
     "counts.plot(kind=\"bar\", log=True)\n",
     "\n",
@@ -293,9 +293,9 @@
     "\n",
     "counts = sel.mother_pdgid_cleaned.value_counts()\n",
     "counts.index = counts.index.map(\n",
-    "    lambda pid: f\"{Particle.from_pdgid(pid).name} ({pid})\"\n",
-    "    if pid != 0\n",
-    "    else \"unknown (0)\"\n",
+    "    lambda pid: (\n",
+    "        f\"{Particle.from_pdgid(pid).name} ({pid})\" if pid != 0 else \"unknown (0)\"\n",
+    "    )\n",
     ")\n",
     "counts.plot(kind=\"bar\", log=True)\n",
     "\n",

docs/examples/plot_spectrum.ipynb

@@ -21,7 +21,6 @@
    "source": [
     "# These modules will be used\n",
     "import numpy as np\n",
-    "import pandas as pd\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "import panama as pn\n",
@@ -247,9 +246,9 @@
     "\n",
     "counts = sel.mother_pdgid_cleaned.value_counts()\n",
     "counts.index = counts.index.map(\n",
-    "    lambda pid: f\"{Particle.from_pdgid(pid).name} ({pid})\"\n",
-    "    if pid != 0\n",
-    "    else \"unknown (0)\"\n",
+    "    lambda pid: (\n",
+    "        f\"{Particle.from_pdgid(pid).name} ({pid})\" if pid != 0 else \"unknown (0)\"\n",
+    "    )\n",
     ")\n",
     "counts.plot(kind=\"bar\", log=True)\n",
     "\n",

panama/_nbstreamreader.py

@@ -4,6 +4,7 @@
 Only to be used internally.
 Adapted from http://eyalarubas.com/python-subproc-nonblock.html
 """
+
 from __future__ import annotations
 
 from queue import Empty, Queue

panama/cli/run.py

@@ -29,7 +29,7 @@ def convert(self, value: int | str, param: Any, ctx: Any) -> int | dict[int, int
             return value
 
         try:
-            d = eval(value)  # noqa: PGH001
+            d = eval(value)
             if not isinstance(d, (int, dict)):  # noqa: UP038
                 self.fail(
                     f"{value!r} is a valid python expression, but not a dict nor an int",

panama/constants.py

@@ -1,6 +1,7 @@
 """
 Some constants used across multiple modules
 """
+
 from particle import PDGID, Particle
 
 D0_LIFETIME = Particle.from_name("D0").lifetime

panama/prompt.py

@@ -2,6 +2,7 @@
 Functions to use to determine if a particle is prompt or not,
 using multiple different definitions.
 """
+
 from __future__ import annotations
 
 from math import inf
@@ -60,9 +61,9 @@ def add_cleaned_mother_cols(df_particles: pd.DataFrame) -> None:
     if "mother_lifetime_cleaned" not in df_particles:
         pdgids = df_particles["mother_pdgid_cleaned"].unique()
         lifetimes = {
-            pdgid: Particle.from_pdgid(pdgid).lifetime
-            if pdgid != PDGID_ERROR_VAL
-            else inf
+            pdgid: (
+                Particle.from_pdgid(pdgid).lifetime if pdgid != PDGID_ERROR_VAL else inf
+            )
             for pdgid in pdgids
         }
         for pdgid in lifetimes:

panama/read.py

@@ -282,9 +282,11 @@ def read_DAT(
         # the use of pd.NA is currently experimental in Int64 type columns
         corsikaids = df_particles["corsikaid"].unique()
         pdg_map = {
-            corsikaid: int(Corsika7ID(corsikaid).to_pdgid())
-            if Corsika7ID(corsikaid).is_particle()
-            else PDGID_ERROR_VAL  # This will be our error value
+            corsikaid: (
+                int(Corsika7ID(corsikaid).to_pdgid())
+                if Corsika7ID(corsikaid).is_particle()
+                else PDGID_ERROR_VAL
+            )  # This will be our error value
             for corsikaid in corsikaids
         }
         df_particles["pdgid"] = (
@@ -381,9 +383,11 @@ def add_mother_columns(
         df_particles.loc[~df_particles["has_mother"], f"mother_{name}"] = error_val
 
     has_charm = {
-        pdgid: "c" in Particle.from_pdgid(pdgid).quarks.lower()
-        if pdgid != PDGID_ERROR_VAL
-        else False
+        pdgid: (
+            "c" in Particle.from_pdgid(pdgid).quarks.lower()
+            if pdgid != PDGID_ERROR_VAL
+            else False
+        )
         for pdgid in pdgids
     }
     # explicitly force an invalid PDGID to not be charm
@@ -401,9 +405,11 @@ def add_mother_columns(
     lifetimes[PDGID_ERROR_VAL] = inf
 
     is_resonance = {
-        pdgid: "*" in Particle.from_pdgid(pdgid).name
-        if pdgid != PDGID_ERROR_VAL
-        else False
+        pdgid: (
+            "*" in Particle.from_pdgid(pdgid).name
+            if pdgid != PDGID_ERROR_VAL
+            else False
+        )
         for pdgid in pdgids
     }
     # explicitly force an invalid PDGID to not be a resonance

panama/run.py

@@ -1,6 +1,7 @@
 """
 Classes handling the parallel execution of CORSIKA7 processes.
 """
+
 from __future__ import annotations
 
 import io

panama/version.py

@@ -2,14 +2,14 @@
 try:
     from importlib.metadata import packages_distributions  # , version
 
-    pkgs = packages_distributions()  # pragma: no cover
-except ImportError:
-    pkgs = {}
+    pkgs = packages_distributions()
+except ImportError:  # pragma: no cover
+    pkgs = {}  # pragma: no cover
 
 __distribution__ = pkgs["panama"][0] if "panama" in pkgs else "corsika-panama"
 
 # __version__ = version(__distribution__)
-__version__ = "1.0.1"
+__version__ = "1.0.2"
 
 LOGO_TEMPLATE = r"""
 ,-.----.                           ,--.das     nd               ____ ulticore utils for corsik  7

panama/weights.py

@@ -4,6 +4,7 @@
 are given in units of :math:`(\mathrm{m^2}\ \mathrm{s}\ \mathrm{sr}\ \mathrm{GeV})^{-1}`.
 
 """  # noqa: W605
+
 from __future__ import annotations
 
 from typing import Any
@@ -150,9 +151,9 @@ def add_weight_prompt(
         df.sort_index(inplace=True)
 
     df[weight_col_name] = 1.0
-    df.loc[
-        df[is_prompt_col_name] == True, weight_col_name  # noqa: E712
-    ] = prompt_factor
+    df.loc[df[is_prompt_col_name] == True, weight_col_name] = (  # noqa: E712
+        prompt_factor
+    )
 
 
 def add_weight_prompt_per_event(