gmxplot 0.2.0__py3-none-any.whl → 0.2.2__py3-none-any.whl

gmxplot/__init__.py

@@ -1,3 +1,3 @@
 """gmxplot - GROMACS XVG file visualization and statistics tool."""
 
-__version__ = "0.2.0"
+__version__ = "0.2.2"

gmxplot/comparison.py

@@ -57,15 +57,26 @@ def _compare_single(datasets: list, labels: list, style: StyleOptions) -> plt.Fi
     multi = len(ds0.y_cols) > 1
     colors = resolve_palette(style.palette, len(datasets))
     fig, ax = plt.subplots(figsize=style.figsize or FIGURE_SIZE_SINGLE)
-    for col in ds0.y_cols:
+    if not multi:
+        # One series per file: match by position, not by column name.  GROMACS
+        # names the legend after the selection, so files that differ only in the
+        # selection (ZF1-DNA, ZF2-DNA, ...) carry different column names and
+        # only the first file would be drawn.
         for i, ds in enumerate(datasets):
-            if col not in ds.y_cols:
+            if not ds.y_cols:
                 continue
-            color = colors[i]
-            label = labels[i] if labels else str(i)
-            if multi:
+            _overlay_line(ax, ds, ds.y_cols[0], colors[i],
+                          labels[i] if labels else str(i), style,
+                          _effective_roll(ds, None))
+    else:
+        for col in ds0.y_cols:
+            for i, ds in enumerate(datasets):
+                if col not in ds.y_cols:
+                    continue
+                color = colors[i]
+                label = labels[i] if labels else str(i)
                 label = f'{label} {col}'
-            _overlay_line(ax, ds, col, color, label, style, _effective_roll(ds, None))
+                _overlay_line(ax, ds, col, color, label, style, _effective_roll(ds, None))
     ax.set_xlabel(_x_title(ds0, style))
     ax.set_ylabel(style.ylabel or ds0.meta.y_label or '')
     ax.set_title(style.title or ds0.meta.title)

gmxplot/plotting.py

@@ -97,16 +97,47 @@ def _make_axes(n_panels: int, figsize: Optional[Tuple[float, float]] = None):
     return fig, axes_flat, n_cols
 
 
+# GROMACS writes ONE y-axis label for a whole multi-column file and merges
+# repeated units: energy.xvg has 6 columns but the label only lists five
+# "(...)" groups.  A purely positional assignment therefore shifts every unit
+# after the duplicate (Total Energy gets K, Temperature gets bar, ...), so fall
+# back to per-term units when the counts do not line up.
+_TERM_UNITS = [
+    (r'\bdensity\b', 'kg/m^3'),
+    (r'\bpressure\b|\bpres\.|\bvir-', 'bar'),
+    (r'\btemperature\b|^t-', 'K'),
+    (r'\bbox-[xyz]\b', 'nm'),
+    (r'\bvolume\b', 'nm^3'),
+    (r'\bpotential\b|\bkinetic\b|\btotal energy\b|\benthalpy\b|\bgibbs\b',
+     'kJ/mol'),
+    (r'\bcoul|\blj-|\bdisper|\bbond|\bangle\b|\bdihedral|\bimproper|\bvdw',
+     'kJ/mol'),
+]
+
+
+def _unit_for_column(col: str, units: List[str]) -> Optional[str]:
+    """Resolve a unit for one column when the file's unit list is incomplete."""
+    label = clean_gromacs_label(col).lower()
+    for pattern, unit in _TERM_UNITS:
+        if re.search(pattern, label):
+            return unit
+    # A single unit for the whole file applies to every column.
+    return units[0] if len(units) == 1 else None
+
+
 def _y_titles(ds: Dataset) -> dict:
     """Map each y column to a display label with units when available."""
-    units = re.findall(r'\(([^()]+)\)', ds.meta.y_label)
+    units = [clean_gromacs_label(u)
+             for u in re.findall(r'\(([^()]+)\)', ds.meta.y_label)]
     out = {}
-    for i, col in enumerate(ds.y_cols):
+    if units and len(units) == len(ds.y_cols):
+        for col, unit in zip(ds.y_cols, units):
+            out[col] = f'{clean_gromacs_label(col)} ({unit})'
+        return out
+    for col in ds.y_cols:
         base = clean_gromacs_label(col)
-        if i < len(units):
-            out[col] = f'{base} ({clean_gromacs_label(units[i])})'
-        else:
-            out[col] = base
+        unit = _unit_for_column(col, units)
+        out[col] = f'{base} ({unit})' if unit else base
     return out
 
 

gmxplot/stats.py

@@ -8,6 +8,7 @@ count-weighted x statistics; PCA analyzes every column (there is no x column).
 import math
 import os
 import re
+from dataclasses import replace
 from pathlib import Path
 from typing import Dict, List, Optional
 
@@ -243,11 +244,10 @@ def generate_stats_csv(
         df, meta = read_xvg(fp)
         if df.empty:
             continue
-        o = opts or DatasetOptions()
-        if not o.label:
-            o.label = os.path.basename(fp)
-        if not o.path:
-            o.path = fp
+        # Per-file copy: mutating a shared options object would pin every later
+        # row to the first file's label/path.
+        label = os.path.basename(fp)
+        o = replace(opts, label=label, path=fp) if opts else DatasetOptions(label=label, path=fp)
         ds = prepare_dataset(df, meta, o)
         bs = block_size
         if block_time is not None and bs is None and ds.x_col is not None:

{gmxplot-0.2.0.dist-info → gmxplot-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: gmxplot
-Version: 0.2.0
+Version: 0.2.2
 Summary: GROMACS XVG visualization and statistics with family/kind semantics, physical time axes, windows, replica aggregation, and dashboards
 Project-URL: Homepage, https://github.com/MaybeBio/gmxplot
 Project-URL: Issues, https://github.com/MaybeBio/gmxplot/issues
@@ -137,6 +137,12 @@ average and drift statistics. Nothing is smoothed by accident.
 
 ## 📦 Installation
 
+```bash
+pip install gmxplot
+```
+
+or
+
 ```bash
 git clone https://github.com/MaybeBio/gmxplot.git
 cd gmxplot

gmxplot-0.2.2.dist-info/RECORD

@@ -0,0 +1,16 @@
+gmxplot/__init__.py,sha256=TThvsrSaI7Y7g1-8vfoj4C14rtS9TCRlCmfNezKUbSo,91
+gmxplot/cli.py,sha256=Z1rdBQ_5swjaXtWzHoodq9JXe0gp0L9pp8-UmTf9L7o,34304
+gmxplot/comparison.py,sha256=wVFmaUYgph9VjtsD8pTT4c3x35ACHB-UiAoMOFbKFEY,5368
+gmxplot/config.py,sha256=9IGso6QluhPKtP204HJjqUUnpq5LVfZcPJTBgeGo190,2696
+gmxplot/dashboard.py,sha256=8tbqgA-o_pYK8DNMusQUeqSp-29XPxt6kgd8b1zFABI,10766
+gmxplot/dataset.py,sha256=bf-823OkOVo1XGCqadj-J5RaRf9genHIibDqdVDXJMc,9399
+gmxplot/escape_codes.py,sha256=HR9F-sy_Jq4NOb74I7bZgUx6svjy2xYHMYTPQRBxBk4,1831
+gmxplot/parser.py,sha256=oijRpBjucRzlMm8OcI4GAkYA6jQAaQ4lzZQZrRwdz7k,10308
+gmxplot/plotting.py,sha256=ujWfJJYAzSaU9xnSO-G48XZIsJci5ajX5E3SkzBMo88,14653
+gmxplot/replicas.py,sha256=eAp3yFZlg1FiY7YVFY7MFYvoXSIPMznj5GjuonVqmkM,7769
+gmxplot/stats.py,sha256=ZuQbdPj4dV2XQfWD9FJZXBSZPFuc478xG7Efjo70Fnk,11496
+gmxplot-0.2.2.dist-info/METADATA,sha256=kgFqDo-8Dqu_vWG69A71O3yrBGYfXYMFj_pevYQG1tg,21701
+gmxplot-0.2.2.dist-info/WHEEL,sha256=W3fkpkm7-wf9vBI5Z-7s0eWkeM-spu78I8Neb98DeEg,87
+gmxplot-0.2.2.dist-info/entry_points.txt,sha256=ENtnfYYCM2sAELFTNdOc2lhOPna_ndmXImWPONbAKRA,44
+gmxplot-0.2.2.dist-info/licenses/LICENSE,sha256=8-mfygEBYs_zUebQalb4qE5TIk8ni9ERmb9g52GWED0,308
+gmxplot-0.2.2.dist-info/RECORD,,

gmxplot-0.2.0.dist-info/RECORD

@@ -1,16 +0,0 @@
-gmxplot/__init__.py,sha256=FGkyYOsuFfy3yx5O9WvX5Q5rSvLfpr7x9Pxp8G3koGg,91
-gmxplot/cli.py,sha256=Z1rdBQ_5swjaXtWzHoodq9JXe0gp0L9pp8-UmTf9L7o,34304
-gmxplot/comparison.py,sha256=gYpIhKin5R7JonYmvC_Bvsaz2pEiV1xYAy6O-ldZaAU,4776
-gmxplot/config.py,sha256=9IGso6QluhPKtP204HJjqUUnpq5LVfZcPJTBgeGo190,2696
-gmxplot/dashboard.py,sha256=8tbqgA-o_pYK8DNMusQUeqSp-29XPxt6kgd8b1zFABI,10766
-gmxplot/dataset.py,sha256=bf-823OkOVo1XGCqadj-J5RaRf9genHIibDqdVDXJMc,9399
-gmxplot/escape_codes.py,sha256=HR9F-sy_Jq4NOb74I7bZgUx6svjy2xYHMYTPQRBxBk4,1831
-gmxplot/parser.py,sha256=oijRpBjucRzlMm8OcI4GAkYA6jQAaQ4lzZQZrRwdz7k,10308
-gmxplot/plotting.py,sha256=nSVjE3M02XLWNhOdpcTaHwtCZ1gotXWqhALJW9KoMpY,13334
-gmxplot/replicas.py,sha256=eAp3yFZlg1FiY7YVFY7MFYvoXSIPMznj5GjuonVqmkM,7769
-gmxplot/stats.py,sha256=2c2V6E6v03PtQEGu6nt3_IdLQO-Q2kGrEnHd6snox6g,11354
-gmxplot-0.2.0.dist-info/METADATA,sha256=RKNLi8WBDf54lLiZTq5OFaoKS8ecT7PFJc_dHrKP-xc,21664
-gmxplot-0.2.0.dist-info/WHEEL,sha256=W3fkpkm7-wf9vBI5Z-7s0eWkeM-spu78I8Neb98DeEg,87
-gmxplot-0.2.0.dist-info/entry_points.txt,sha256=ENtnfYYCM2sAELFTNdOc2lhOPna_ndmXImWPONbAKRA,44
-gmxplot-0.2.0.dist-info/licenses/LICENSE,sha256=8-mfygEBYs_zUebQalb4qE5TIk8ni9ERmb9g52GWED0,308
-gmxplot-0.2.0.dist-info/RECORD,,