Allow Co57 and Ni57 columns in downscale3dgrid (#70)

.github/workflows/linter.yml

@@ -15,28 +15,6 @@ jobs:
               with:
                   options: --check --verbose
 
-    flake8:
-        runs-on: ubuntu-latest
-        steps:
-            - name: Checkout Code
-              uses: actions/checkout@v3
-
-            - name: Set up Python
-              uses: actions/setup-python@v4
-              with:
-                  cache: pip
-                  python-version-file: .python-version
-
-            - name: Install dependencies
-              run: |
-                  python3 -m pip install --upgrade pip wheel flake8
-                  # python3 -m pip install -r requirements.txt
-
-            - name: Lint with flake8
-              run: |
-                  # stop the build if there are Python syntax errors or undefined names
-                  flake8 . --count --show-source --statistics
-
     mypy:
         runs-on: ubuntu-latest
         steps:

.pre-commit-config.yaml

@@ -29,22 +29,16 @@ repos:
       hooks:
           - id: yamlfmt
     - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.265
+      rev: v0.0.267
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]
-    - repo: https://github.com/asottile/reorder_python_imports
-      rev: v3.9.0
-      hooks:
-          - id: reorder-python-imports
-            types: [python]
-            args: [--py39-plus, --exit-zero-even-if-changed]
     - repo: https://github.com/psf/black
       rev: 23.3.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.2.0
+      rev: v1.3.0
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-PyYAML, types-psutil]

artistools/__init__.py

@@ -19,6 +19,7 @@
 import artistools.spectra
 import artistools.transitions
 import artistools.writecomparisondata
+
 from .__main__ import addargs
 from .__main__ import main
 from .configuration import get_config

artistools/__main__.py

@@ -5,11 +5,11 @@
 
 import argcomplete
 
-from .commands import dictcommands
+from .commands import dictcommands as atdictcommands
 from .misc import CustomArgHelpFormatter
 
 
-def addargs(parser=None) -> None:
+def addargs(parser: argparse.ArgumentParser) -> None:
     pass
 
 
@@ -49,7 +49,7 @@ def main(args=None, argsraw=None, **kwargs) -> None:
     )
     parser.set_defaults(func=None)
 
-    addsubparsers(parser, "artistools", dictcommands)
+    addsubparsers(parser, "artistools", atdictcommands)
 
     argcomplete.autocomplete(parser)
     args = parser.parse_args(argsraw)

artistools/commands.py

@@ -1,5 +1,7 @@
+import argparse
 import subprocess
 from pathlib import Path
+from typing import Any
 from typing import Union
 
 try:
@@ -118,7 +120,7 @@ def get_console_scripts() -> list[str]:
     return console_scripts
 
 
-def setup_completions(*args, **kwargs) -> None:
+def setup_completions(*args: Any, **kwargs: Any) -> None:
     # Add the following lines to your .zshrc file to get command completion:
     # autoload -U bashcompinit
     # bashcompinit
@@ -148,5 +150,5 @@ def setup_completions(*args, **kwargs) -> None:
     print("source artistoolscompletions.sh")
 
 
-def addargs(parser=None) -> None:
+def addargs(parser: argparse.ArgumentParser) -> None:
     pass

artistools/estimators/estimators_classic.py

@@ -10,17 +10,17 @@ def get_atomic_composition(modelpath):
     """Read ion list from output file."""
     atomic_composition = {}
 
-    output = open(modelpath / "output_0-0.txt").read().splitlines()
-    ioncount = 0
-    for row in output:
-        if row.split()[0] == "[input.c]":
-            split_row = row.split()
-            if split_row[1] == "element":
-                Z = int(split_row[4])
-                ioncount = 0
-            elif split_row[1] == "ion":
-                ioncount += 1
-                atomic_composition[Z] = ioncount
+    with open(modelpath / "output_0-0.txt") as foutput:
+        ioncount = 0
+        for row in foutput:
+            if row.split()[0] == "[input.c]":
+                split_row = row.split()
+                if split_row[1] == "element":
+                    Z = int(split_row[4])
+                    ioncount = 0
+                elif split_row[1] == "ion":
+                    ioncount += 1
+                    atomic_composition[Z] = ioncount
     return atomic_composition
 
 

artistools/hesma_scripts.py

@@ -14,7 +14,7 @@ def plot_hesma_spectrum(timeavg, axes):
     # print(hesma_spec)
 
     def match_closest_time(reftime):
-        return str("{}".format(min([float(x) for x in hesma_spec.keys()[1:]], key=lambda x: abs(x - reftime))))
+        return str(f"{min([float(x) for x in hesma_spec.keys()[1:]], key=lambda x: abs(x - reftime))}")
 
     closest_time = match_closest_time(timeavg)
     closest_time = f"{closest_time:.2f}"

artistools/inputmodel/1dslicefrom3d.py

@@ -3,6 +3,7 @@
 import math
 import os
 import sys
+from pathlib import Path
 
 import matplotlib.pyplot as plt
 
@@ -33,12 +34,12 @@ def main(args=None, argsraw=None, **kwargs):
         parser.set_defaults(**kwargs)
         args = parser.parse_args()
 
-    if not os.path.exists(args.outputfolder):
-        os.makedirs(args.outputfolder)
-    elif os.path.exists(os.path.join(args.outputfolder, "model.txt")):
+    if not Path(args.outputfolder).exists():
+        Path(args.outputfolder).mkdir(parents=True)
+    elif Path(args.outputfolder, "model.txt").exists():
         print("ABORT: model.txt already exists")
         sys.exit()
-    elif os.path.exists(os.path.join(args.outputfolder, "abundances.txt")):
+    elif Path(args.outputfolder, "abundances.txt").exists():
         print("ABORT: abundances.txt already exists")
         sys.exit()
 

artistools/inputmodel/__init__.py

@@ -7,6 +7,7 @@
 import artistools.inputmodel.modelfromhydro
 import artistools.inputmodel.opacityinputfile
 import artistools.inputmodel.rprocess_from_trajectory
+
 from .inputmodel_misc import add_derived_cols_to_modeldata
 from .inputmodel_misc import get_2d_modeldata
 from .inputmodel_misc import get_3d_model_data_merged_model_and_abundances_minimal