Remove setup.py (#158)

.github/workflows/deploypypi.yml

@@ -22,7 +22,6 @@ jobs:
             - name: Install dependencies
               run: |
                   python3 -m pip install --upgrade pip
-                  python3 -m pip install -r requirements.txt
                   python3 -m pip install --upgrade setuptools setuptools_scm[toml] wheel twine build
 
             - name: Build

.github/workflows/deploytestpypi.yml

@@ -27,7 +27,6 @@ jobs:
             - name: Install dependencies
               run: |
                   python3 -m pip install --upgrade pip
-                  python3 -m pip install -r requirements.txt
                   python3 -m pip install --upgrade setuptools setuptools_scm[toml] wheel twine build
 
             - name: Build

.github/workflows/pytest.yml

@@ -37,11 +37,18 @@ jobs:
               with:
                   python-version: ${{ matrix.python-version }}
 
+            - name: Cache venv
+              uses: actions/cache@v4
+              with:
+                  path: .venv
+                  key: py${{ matrix.python-version }}-venv
+
             - name: Install artistools
               run: |
                   python3 -m pip install --upgrade uv
-                  uv venv
+                  if [ ! -d ".venv" ]; then uv venv .venv; fi
                   source .venv/bin/activate
+                  echo "PATH=$PWD/.venv/bin:$PATH" >> $GITHUB_ENV
                   uv pip install -e .
 
             - name: Cache test data
@@ -54,6 +61,11 @@ jobs:
               working-directory: tests/data/
               run: source ./setuptestdata.sh
 
+            - name: Check artistools command line tool
+              run: |
+                  .venv/bin/artistools --help
+                  .venv/bin/artistools setupcompletions
+
             - name: Test with pytest
               run: |
                   source .venv/bin/activate

MANIFEST.in

@@ -1,8 +1,15 @@
 recursive-include artistools *.csv
 recursive-include artistools *.txt
 recursive-include artistools matplotlibrc
-global-include *.pyi
-global-include *.typed
 global-include *.md
 global-include *.cff
-include LICENSE.txt
+include LICENSE.txt
+recursive-exclude dist *
+recursive-exclude build *
+prune **/.*
+prune **/*.egg*
+prune tests
+prune build
+prune lib
+prune dist
+prune images

artistools/__main__.py

@@ -8,20 +8,20 @@
 import argcomplete
 
 from artistools.commands import CommandType
-from artistools.commands import dictcommands as atdictcommands
+from artistools.commands import subcommandtree as atdictcommands
 from artistools.misc import CustomArgHelpFormatter
 
 
 def addsubparsers(
-    parser: argparse.ArgumentParser, parentcommand: str, dictcommands: CommandType, depth: int = 1
+    parser: argparse.ArgumentParser, parentcommand: str, subcommandtree: CommandType, depth: int = 1
 ) -> None:
     def func(args: t.Any) -> None:
         parser.print_help()
 
     parser.set_defaults(func=func)
     subparsers = parser.add_subparsers(dest=f"{parentcommand} command", required=False)
 
-    for subcommand, subcommands in dictcommands.items():
+    for subcommand, subcommands in subcommandtree.items():
         strhelp: str | None
         if isinstance(subcommands, dict):
             strhelp = "command group"
@@ -40,7 +40,7 @@ def func(args: t.Any) -> None:
             subparser.set_defaults(func=func)
         else:
             assert not isinstance(subcommands, tuple)
-            addsubparsers(parser=subparser, parentcommand=subcommand, dictcommands=subcommands, depth=depth + 1)
+            addsubparsers(parser=subparser, parentcommand=subcommand, subcommandtree=subcommands, depth=depth + 1)
 
 
 def addargs(parser: argparse.ArgumentParser) -> None:

artistools/commands.py

@@ -3,10 +3,32 @@
 import typing as t
 from pathlib import Path
 
+# top-level commands (one file installed per command)
+# we generally should phase this out except for a couple of main ones like at and artistools
+COMMANDS = [
+    "at",
+    "artistools",
+    "makeartismodel1dslicefromcone",
+    "makeartismodel",
+    "plotartisdensity",
+    "plotartisdeposition",
+    "plotartisestimators",
+    "plotartislightcurve",
+    "plotartislinefluxes",
+    "plotartismacroatom",
+    "plotartisnltepops",
+    "plotartisnonthermal",
+    "plotartisradfield",
+    "plotartisspectrum",
+    "plotartistransitions",
+    "plotartisinitialcomposition",
+    "plotartisviewingangles",
+]
+
 CommandType: t.TypeAlias = dict[str, t.Union[tuple[str, str], "CommandType"]]
 
 # new subparser based list
-dictcommands: CommandType = {
+subcommandtree: CommandType = {
     "comparetogsinetwork": ("gsinetwork", "main"),
     "deposition": ("deposition", "main_analytical"),
     "describeinputmodel": ("inputmodel.describeinputmodel", "main"),
@@ -52,36 +74,6 @@
 }
 
 
-def get_commandlist() -> dict[str, tuple[str, str]]:
-    # direct commands (one file installed per command)
-    # we generally should phase this out except for a couple of main ones like at and artistools
-    return {
-        "at": ("artistools", "main"),
-        "artistools": ("artistools", "main"),
-        "makeartismodel1dslicefromcone": ("artistools.inputmodel.slice1dfromconein3dmodel", "main"),
-        "makeartismodel": ("artistools.inputmodel.makeartismodel", "main"),
-        "plotartisdensity": ("artistools.inputmodel.plotdensity", "main"),
-        "plotartisdeposition": ("artistools.deposition", "main"),
-        "plotartisestimators": ("artistools.estimators.plotestimators", "main"),
-        "plotartislightcurve": ("artistools.lightcurve.plotlightcurve", "main"),
-        "plotartislinefluxes": ("artistools.linefluxes", "main"),
-        "plotartismacroatom": ("artistools.macroatom", "main"),
-        "plotartisnltepops": ("artistools.nltepops.plotnltepops", "main"),
-        "plotartisnonthermal": ("artistools.nonthermal", "main"),
-        "plotartisradfield": ("artistools.radfield", "main"),
-        "plotartisspectrum": ("artistools.spectra.plotspectra", "main"),
-        "plotartistransitions": ("artistools.transitions", "main"),
-        "plotartisinitialcomposition": ("artistools.inputmodel.plotinitialcomposition", "main"),
-        "plotartisviewingangles": ("artistools.viewing_angles_visualization", "main"),
-    }
-
-
-def get_console_scripts() -> list[str]:
-    return [
-        f"{command} = {submodulename}:{funcname}" for command, (submodulename, funcname) in get_commandlist().items()
-    ]
-
-
 def setup_completions(*args: t.Any, **kwargs: t.Any) -> None:
     # Add the following lines to your .zshrc file to get command completion:
     # autoload -U bashcompinit
@@ -105,7 +97,7 @@ def setup_completions(*args: t.Any, **kwargs: t.Any) -> None:
         f.write(strsplit)
         f.write("\n\n")
 
-        for command in get_commandlist():
+        for command in COMMANDS:
             completecommand = strcommandregister.replace("__MY_COMMAND__", command)
             f.write(completecommand + "\n")
 

artistools/nonthermal/_nonthermal_core.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-
+import argparse
 import math
 from collections import namedtuple
 from math import atan
@@ -284,7 +284,7 @@ def lossfunction(energy_ev, nne_cgs):
     return lossfunc / EV  # return as [eV / cm]
 
 
-def Psecondary(e_p, ionpot_ev, J, e_s=-1, epsilon=-1):
+def Psecondary(e_p: float, ionpot_ev: float, J: float, e_s: float = -1, epsilon: float = -1) -> float:
     # probability distribution function for secondaries energy e_s [eV] (or equivalently the energy loss of
     # the primary electron epsilon [eV]) given a primary energy e_p [eV] for an impact ionisation event
 
@@ -1257,7 +1257,7 @@ def calculate_Latom_ionisation(ions, ionpopdict, dfcollion, nntot, nne, en_ev, n
     return L_atom_sum
 
 
-def workfunction_tests(modelpath, args):
+def workfunction_tests(modelpath: str | Path, args: argparse.Namespace) -> None:
     electron_binding = read_binding_energies()
     dfcollion = at.nonthermal.read_colliondata()
 
@@ -1266,14 +1266,11 @@ def workfunction_tests(modelpath, args):
     )
     axes = [axes]
 
-    ionpopdict = {
-        # (16, 2): 3e5,
+    ionpopdict: dict[tuple[int, int], float] = {
         (26, 2): 1e5,
     }
 
-    # keep only the ion populations, not element or total populations
-    ions = [key for key in ionpopdict if isinstance(key, tuple) and len(key) == 2]
-    ions.sort()
+    ions = sorted(ionpopdict.keys())
 
     nntot = get_nntot(ions=ions, ionpopdict=ionpopdict)
     nnetot = get_nnetot(ions=ions, ionpopdict=ionpopdict)  # total electrons: free and bound included
@@ -1454,7 +1451,9 @@ def workfunction_tests(modelpath, args):
         integrand = arr_xs / (L / EV)
         # arr_workfn_integrated[i] is the en_ev / (integral xs / L dE from EMIN to E[i])
         with np.errstate(divide="ignore"):
-            arr_workfn_integrated = [arr_en_ev[i] / (sum((integrand * delta_en_ev)[:i])) for i in range(len(arr_en_ev))]
+            arr_workfn_integrated = np.array(
+                [arr_en_ev[i] / (sum((integrand * delta_en_ev)[:i])) for i in range(len(arr_en_ev))]
+            )
 
         print(f"\n workfn_integral_Emin_Emax: {arr_workfn_integrated[-1]:.2f} eV")
         print(f"   eta_ion  {ionpot_valence_ev / arr_workfn_integrated[-1]:.3f}")

artistools/test_artistools.py

@@ -1,9 +1,11 @@
 #!/usr/bin/env python3
+import contextlib
 import hashlib
 import importlib
 import inspect
 import math
 import typing as t
+from pathlib import Path
 
 import artistools as at
 
@@ -23,12 +25,21 @@ def funcname() -> str:
 
 
 def test_commands() -> None:
-    # ensure that the commands are pointing to valid submodule.function() targets
-    for _command, (submodulename, funcname) in sorted(at.commands.get_commandlist().items()):
-        submodule = importlib.import_module(submodulename)
-        assert hasattr(submodule, funcname) or (
-            funcname == "main" and hasattr(importlib.import_module(f"{submodulename}.__main__"), funcname)
-        )
+    commands: dict[str, tuple[str, str]] = {}
+
+    with contextlib.suppress(ImportError):
+        import tomllib
+
+        with Path("pyproject.toml").open("rb") as f:
+            pyproj = tomllib.load(f)
+        commands = {k: tuple(v.split(":")) for k, v in pyproj["project"]["scripts"].items()}
+
+        # ensure that the commands are pointing to valid submodule.function() targets
+        for command, (submodulename, funcname) in commands.items():
+            submodule = importlib.import_module(submodulename)
+            assert hasattr(submodule, funcname) or (
+                funcname == "main" and hasattr(importlib.import_module(f"{submodulename}.__main__"), funcname)
+            ), f"{submodulename}.{funcname} not found for command {command}"
 
     def recursive_check(dictcmd: dict[str, t.Any]) -> None:
         for cmdtarget in dictcmd.values():
@@ -43,7 +54,7 @@ def recursive_check(dictcmd: dict[str, t.Any]) -> None:
                     funcname == "main" and hasattr(importlib.import_module(f"{namestr}.__main__"), funcname)
                 )
 
-    recursive_check(at.commands.dictcommands)
+    recursive_check(at.commands.subcommandtree)
 
 
 def test_timestep_times() -> None: