Fix h5part reader and add venv install script

tools/h5part_reader.py

@@ -17,8 +17,7 @@
 import h5py
 import numpy as np
 
-from pydrex import core as _core
-from pydrex import minerals as _minerals
+from pydrex import Mineral, MineralFabric, MineralPhase
 
 
 def _get_args() -> argparse.Namespace:
@@ -76,14 +75,14 @@ def _get_args() -> argparse.Namespace:
 
         for particle_id in file["Step#0/id"][:]:
             option_map = {
-                "olivine": _core.MineralPhase.olivine,
-                "enstatite": _core.MineralPhase.enstatite,
-                "A": _minerals.OlivineFabric.A,
-                "B": _minerals.OlivineFabric.B,
-                "C": _minerals.OlivineFabric.C,
-                "D": _minerals.OlivineFabric.D,
-                "E": _minerals.OlivineFabric.E,
-                "N": _minerals.EnstatiteFabric.A,
+                "olivine": MineralPhase.olivine,
+                "enstatite": MineralPhase.enstatite,
+                "A": MineralFabric.olivine_A,
+                "B": MineralFabric.olivine_B,
+                "C": MineralFabric.olivine_C,
+                "D": MineralFabric.olivine_D,
+                "E": MineralFabric.olivine_E,
+                "N": MineralFabric.enstatite_AB,
             }
 
             # Temporary data arrays.
@@ -115,7 +114,7 @@ def _get_args() -> argparse.Namespace:
             _postfix = str(particle_id)
             _fractions = list(fractions)
             _orientations = list(orientations)
-            mineral = _minerals.Mineral(
+            mineral = Mineral(
                 phase=option_map[args.fabric],
                 fabric=option_map[args.phase],
                 n_grains=args.ngrains,

tools/venv_install.sh

@@ -0,0 +1,44 @@
+#!/bin/env sh
+set -eu
+readonly SCRIPTNAME="${0##*/}"
+usage() {
+    printf 'Usage: %s [-h]\n' "$SCRIPTNAME"
+    printf '       %s [-u]\n' "$SCRIPTNAME"
+}
+helpf() {
+    echo 'Options:'
+    echo '-u            Update pydrex and dependencies in the venv'
+    echo '              and compile new requirements.txt'
+    echo
+    echo 'Install local pydrex tree in a Python venv (virtual environment),'
+    echo 'in editable mode with development dependencies.'
+    echo 'This script should be executed in a context which has access to a'
+    echo 'Python binary of the appropriate version (check requires-python in'
+    echo 'pyproject.toml). If the necessary version is not available on your'
+    echo 'system, you can install it using pyenv'
+    echo '(https://github.com/pyenv/pyenv) and this script will prefer the'
+    echo 'local pyenv binary over the system one.'
+    echo
+    echo 'Backups of the last requirements.txt are stored in requirements.bak'
+}
+
+upgrade() {
+    . .venv-"${PWD##*/}"/bin/activate
+    [ -f requirements.txt ] && mv -i requirements.txt requirements.bak
+    pip install --upgrade pip pip-tools && pip-compile --resolver=backtracking && pip-sync
+    pip install -e "$PWD"\[dev\]
+}
+
+if [ $# -eq 0 ]; then  # first install
+    [ -d .venv-"${PWD##*/}" ] && exit 0  # venv already exists, no-op
+    "$(2>/dev/null pyenv prefix||printf '/usr')"/bin/python -m venv .venv-"${PWD##*/}"
+    upgrade
+fi
+
+while getopts "hu" OPT; do
+    case $OPT in
+        h ) usage && helpf; exit 0;;
+        u ) upgrade;;
+        * ) usage; exit 1;;
+    esac
+done