cellpy 2.0.0a2__tar.gz → 2.0.0a3__tar.gz

cellpy-2.0.0a3/.issueflows/03-solved-issues/issue537_original.md

@@ -0,0 +1,28 @@
+# Issue #537: v2 pre-flip: replace hardcoded journal-page column literals with HeadersJournal
+
+Source: https://github.com/jepegit/cellpy/issues/537
+
+## Original issue text
+
+## Context
+
+Phase-3 flip prerequisite (native-headers plan Phase 0, item 2; hardcoded-column-headers-report §8 priority 1). Audited 2026-07-17 with `.issueflows/00-tools/scan_hardcoded_headers.py`; remaining `HeadersJournal`-family findings:
+
+| File | Findings (all families) |
+|---|---|
+| `cellpy/utils/batch_tools/batch_plotters.py` | 32 |
+| `cellpy/utils/helpers.py` | 34 (journal subset only in this issue) |
+| `cellpy/utils/collectors.py` | 16 (journal subset) |
+| `cellpy/utils/batch_tools/batch_journals.py` | 1 |
+| `cellpy/utils/batch.py` | 0 — already clean, keep it that way |
+
+## Work
+
+Mechanical 1:1: each literal flagged as `HeadersJournal` by the scan tool becomes an attribute access on the already-imported `hdr_journal` / `get_headers_journal()`. No behavior change. Leave non-journal findings in the same files for the sibling issue (steps/raw/summary literals).
+
+## Acceptance
+
+- [ ] Scan tool reports **zero `HeadersJournal` findings** for the files above
+- [ ] Full suite green (behavior unchanged — this is a pure rename-to-lookup)
+
+🤖 Generated with [Claude Code](https://claude.com/claude-code)

cellpy-2.0.0a3/.issueflows/03-solved-issues/issue537_plan.md

@@ -0,0 +1,38 @@
+# Issue #537 plan — journal-page column literals → HeadersJournal
+
+## Goal
+
+Remove the hard-coded journal column-name string literals flagged by
+`.issueflows/00-tools/scan_hardcoded_headers.py` as `HeadersJournal`, so a
+later header rename touches the header class only (native-headers Phase-0
+prerequisite).
+
+## Scope (verified with the scan tool, 2026-07-17)
+
+Only **6 findings, on 3 lines** — all are string-keyed subscripts into the
+already-imported `hdr_journal` object (the §6 "semi-sanctioned" pattern):
+
+- `cellpy/utils/batch_tools/batch_plotters.py:53` — `hdr_journal["mass"]`,
+  `["loading"]`, `["label"]`
+- `cellpy/utils/batch_tools/batch_plotters.py:76` — `hdr_journal["group"]`,
+  `["sub_group"]`
+- `cellpy/utils/helpers.py:278` — `hdr_journal["loading"]`
+
+Non-journal (raw/steps/summary) literals in the same files are **out of
+scope** — they belong to #538.
+
+## Approach
+
+Mechanical `hdr_journal["<name>"]` → `hdr_journal.<name>`. Verified all five
+attribute values equal their subscript values (`HeadersJournal` is a dataclass
+exposing both), so behavior is byte-identical.
+
+## Files to touch
+
+- `cellpy/utils/batch_tools/batch_plotters.py`
+- `cellpy/utils/helpers.py`
+
+## Test strategy
+
+Behavior-preserving rename-to-lookup; the full suite is the oracle. Confirm
+the scan tool reports **zero `HeadersJournal` findings** for both files after.

cellpy-2.0.0a3/.issueflows/03-solved-issues/issue537_status.md

@@ -0,0 +1,27 @@
+# Issue #537 status — journal-page column literals → HeadersJournal
+
+- [x] Done
+
+## Outcome
+
+All 6 `HeadersJournal` scan findings removed (3 lines):
+
+- `cellpy/utils/batch_tools/batch_plotters.py` — `hdr_journal["mass"|"loading"|"label"]`
+  and `["group"|"sub_group"]` → attribute access.
+- `cellpy/utils/helpers.py` — `hdr_journal["loading"]` → `hdr_journal.loading`.
+
+Scan tool now reports **0 `HeadersJournal` findings** for both files.
+
+## Verification
+
+- Attribute values confirmed equal to subscript values (byte-identical behavior).
+- `tests/test_batch.py` + `tests/test_helpers.py`: 58 passed post-edit.
+- Full suite baseline green (668 passed; the single Windows-only HDF5
+  `driver lock request failed` setup error on `test_has_no_full_duplicates` is
+  a pre-existing test-isolation flake — passes in isolation, not on the Linux
+  CI gate).
+- ruff: no new findings vs master.
+
+## Out of scope (other issues)
+
+- Raw/steps/summary literals in the same files → #538.

{cellpy-2.0.0a2 → cellpy-2.0.0a3}/DEPRECATIONS.md

@@ -8,5 +8,4 @@ uv run python -m cellpy._deprecation
 
 | Name | Replacement | Introduced | Removal |
 | --- | --- | --- | --- |
-| `cellpy.utils.easyplot` | `cellpy.utils.plotutils and cellpy.utils.collectors` | 1.1 | 2.0 |
 | `make_new_cell` | `CellpyCell.vacant` | 2.0 | 2.1 |

{cellpy-2.0.0a2 → cellpy-2.0.0a3}/HISTORY.md

@@ -2,6 +2,32 @@
 
 ## [Unreleased]
 
+* Removed the deprecated `cellpy.utils.easyplot` module (#544). It was
+  deprecated since 1.1 with removal scheduled for 2.0; use
+  `cellpy.utils.plotutils` and `cellpy.utils.collectors` instead. The module,
+  its tests, its docs entry, and its `DEPRECATIONS.md` row are gone.
+
+* Step-type string literals use the `cellpycore` vocabulary (#543, native-
+  headers Phase-0 prerequisite): `CellpyCell.list_of_step_types` is now
+  `list(config.STEP_TYPES)` (was a hand-maintained duplicate of the 13
+  step-type names), and the step-table `type` comparisons in `utils/ocv_rlx.py`
+  / `utils/helpers.py` use `StepType.CHARGE.value` / `.DISCHARGE.value` instead
+  of bare `"charge"` / `"discharge"` literals. Behavior-identical.
+
+* Header column literals in `utils/helpers.py` and `filters/summary.py` use
+  header-object attributes (#538, native-headers Phase-0 prerequisite): the
+  base-name string-keyed `hdr_summary["charge_capacity"]`-style lookups become
+  attribute access, and `filter_summary`'s `rate_columns` default is resolved
+  from `HeadersSummary` (was a hard-coded `("charge_c_rate", "discharge_c_rate")`
+  tuple). Postfix/specific columns (`*_gravimetric`, `areal_*`) keep string-key
+  composition. Behavior-identical.
+
+* Journal-page column literals use `HeadersJournal` attributes (#537, native-
+  headers Phase-0 prerequisite): the string-keyed `hdr_journal["mass"]`-style
+  lookups in `batch_plotters.py` and `helpers.py` become attribute access
+  (`hdr_journal.mass`, …) so a journal-header rename touches the header class
+  only. Behavior-identical.
+
 * Remote paths via `universal_pathlib` (#375, #371): `OtherPath` is now a thin
   wrapper around `UPath` (fsspec/Paramiko) instead of Fabric. Supported schemes
   remain `ssh://` / `sftp://` / `scp://` (scp aliased to sftp). Remote

{cellpy-2.0.0a2 → cellpy-2.0.0a3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellpy
-Version: 2.0.0a2
+Version: 2.0.0a3
 Summary: Extract and manipulate data from battery data testers.
 Project-URL: Homepage, https://github.com/jepegit/cellpy
 Project-URL: Repository, https://github.com/jepegit/cellpy

{cellpy-2.0.0a2 → cellpy-2.0.0a3}/cellpy/_deprecation.py

@@ -94,12 +94,8 @@ def write_deprecations_md(path: str | Path) -> None:
 def _seed_known_deprecations() -> None:
     """Register deprecations that exist before any runtime call (for doc generation)."""
     _register("make_new_cell", "CellpyCell.vacant", removal="2.1")
-    _register(
-        "cellpy.utils.easyplot",
-        "cellpy.utils.plotutils and cellpy.utils.collectors",
-        removal="2.0",
-        introduced="1.1",
-    )
+    # cellpy.utils.easyplot was removed in 2.0 (#544); it is no longer a
+    # pending deprecation, so it is dropped from the registry / DEPRECATIONS.md.
 
 
 if __name__ == "__main__":

{cellpy-2.0.0a2 → cellpy-2.0.0a3}/cellpy/filters/summary.py

@@ -29,6 +29,8 @@ import logging
 from collections.abc import Mapping, Sequence
 from typing import Any, Callable, Optional, Union
 
+from cellpy.parameters.internal_settings import get_headers_summary
+
 import pandas as pd
 
 logger = logging.getLogger(__name__)
@@ -145,7 +147,7 @@ def filter_summary(
     df: pd.DataFrame,
     *,
     rate: RangeArg = None,
-    rate_columns: ColumnsArg = ("charge_c_rate", "discharge_c_rate"),
+    rate_columns: ColumnsArg = None,
     **extra_filters: Any,
 ) -> pd.DataFrame:
     """Filter rows of a cellpy summary DataFrame.
@@ -159,6 +161,8 @@ def filter_summary(
             mapping ``{"value": v, "delta": d}`` (keep rows with
             ``v - d < value <= v + d``).
         rate_columns: Which column(s) the ``rate`` filter applies to.
+            ``None`` (default) resolves to the summary C-rate columns
+            (``HeadersSummary.charge_c_rate`` / ``.discharge_c_rate``).
             A single string is coerced to a one-element tuple. With more
             than one column the predicate is AND-ed across columns - a
             row is kept only if *every* listed column lies in range.
@@ -176,6 +180,10 @@ def filter_summary(
             argument is malformed.
         TypeError: A range argument has an unsupported type.
     """
+    if rate_columns is None:
+        hdr_summary = get_headers_summary()
+        rate_columns = (hdr_summary.charge_c_rate, hdr_summary.discharge_c_rate)
+
     range_kwargs = {k: v for k, v in extra_filters.items() if not k.endswith("_columns")}
     column_kwargs = {k: v for k, v in extra_filters.items() if k.endswith("_columns")}
 

{cellpy-2.0.0a2 → cellpy-2.0.0a3}/cellpy/readers/cellreader.py

@@ -58,6 +58,7 @@ from cellpy.parameters.internal_settings import (
 # still expects. cellpy-core's __init__ is intentionally empty, so import submodules.
 from cellpycore import units as core_units
 from cellpycore.cell_core import OldCellpyCellCore
+from cellpycore.config import STEP_TYPES
 
 from cellpy.readers.cellpy_file import dtype as cellpy_file_dtype
 from cellpy.readers.cellpy_file import fids as cellpy_file_fids
@@ -297,21 +298,9 @@ class CellpyCell:
 
         self.capacity_modifiers = ["reset"]
 
-        self.list_of_step_types = [
-            "charge",
-            "discharge",
-            "cv_charge",
-            "cv_discharge",
-            "taper_charge",
-            "taper_discharge",
-            "charge_cv",
-            "discharge_cv",
-            "ocvrlx_up",
-            "ocvrlx_down",
-            "ir",
-            "rest",
-            "not_known",
-        ]
+        # single source of the step-type vocabulary (cellpycore #543);
+        # was a hand-maintained duplicate of config.STEP_TYPES.
+        self.list_of_step_types = list(STEP_TYPES)
         # - options
         self.force_step_table_creation = config.reader.force_step_table_creation
         self.force_all = config.reader.force_all

{cellpy-2.0.0a2 → cellpy-2.0.0a3}/cellpy/utils/batch_tools/batch_plotters.py

@@ -50,7 +50,7 @@ def create_legend(info, c, option="clean", use_index=False):
 
     logging.debug("    - creating legends")
     mass, loading, label = info.loc[
-        c, [hdr_journal["mass"], hdr_journal["loading"], hdr_journal["label"]]
+        c, [hdr_journal.mass, hdr_journal.loading, hdr_journal.label]
     ]
 
     if use_index or not label:
@@ -73,7 +73,7 @@ def create_legend(info, c, option="clean", use_index=False):
 
 def look_up_group(info, c):
     logging.debug("    - looking up groups")
-    g, sg = info.loc[c, [hdr_journal["group"], hdr_journal["sub_group"]]]
+    g, sg = info.loc[c, [hdr_journal.group, hdr_journal.sub_group]]
     return int(g), int(sg)
 
 

{cellpy-2.0.0a2 → cellpy-2.0.0a3}/cellpy/utils/helpers.py

@@ -9,6 +9,8 @@ import numpy as np
 import pandas as pd
 from scipy import stats
 
+from cellpycore.config import StepType
+
 import cellpy
 import cellpy.config as config
 from cellpy import prms
@@ -37,8 +39,8 @@ def _make_average_legacy(
 ):
     if key_index_bounds is None:
         key_index_bounds = [1, -2]
-    hdr_norm_cycle = hdr_summary["normalized_cycle_index"]
-    hdr_cum_charge = hdr_summary["cumulated_charge_capacity"]
+    hdr_norm_cycle = hdr_summary.normalized_cycle_index
+    hdr_cum_charge = hdr_summary.cumulated_charge_capacity
     cell_id = ""
     not_a_number = np.nan
     new_frames = []
@@ -103,7 +105,7 @@ def _make_average(
     skip_st_dev_for_equivalent_cycle_index=True,
     average_method="mean",
 ):
-    hdr_norm_cycle = hdr_summary["normalized_cycle_index"]
+    hdr_norm_cycle = hdr_summary.normalized_cycle_index
     not_a_number = np.nan
     new_frames = []
 
@@ -225,7 +227,7 @@ def add_normalized_cycle_index(summary, nom_cap, column_name=None):
     Returns:
         data object now with normalized cycle index in its summary.
     """
-    hdr_norm_cycle = hdr_summary["normalized_cycle_index"]
+    hdr_norm_cycle = hdr_summary.normalized_cycle_index
     hdr_cum_charge = hdr_summary["cumulated_charge_capacity_gravimetric"]
 
     if column_name is None:
@@ -260,7 +262,7 @@ def add_c_rate(cell, nom_cap=None, column_name=None):
     # now also included in step_table
     # TODO: remove this function
     if column_name is None:
-        column_name = hdr_steps["rate_avr"]
+        column_name = hdr_steps.rate_avr
     if nom_cap is None:
         nom_cap = cell.data.nom_cap
 
@@ -275,13 +277,13 @@ def add_c_rate(cell, nom_cap=None, column_name=None):
 def add_areal_capacity(cell, cell_id, journal):
     """Adds areal capacity to the summary."""
 
-    loading = journal.pages.loc[cell_id, hdr_journal["loading"]]
+    loading = journal.pages.loc[cell_id, hdr_journal.loading]
 
     cell.data.summary[hdr_summary["areal_charge_capacity"]] = (
-        cell.data.summary[hdr_summary["charge_capacity"]] * loading / 1000
+        cell.data.summary[hdr_summary.charge_capacity] * loading / 1000
     )
     cell.data.summary[hdr_summary["areal_discharge_capacity"]] = (
-        cell.data.summary[hdr_summary["discharge_capacity"]] * loading / 1000
+        cell.data.summary[hdr_summary.discharge_capacity] * loading / 1000
     )
     return cell
 
@@ -303,7 +305,7 @@ def remove_outliers_from_summary_on_window(
 ):
     """Removes outliers based on neighbours"""
     if col_name is None:
-        col = hdr_summary["charge_capacity"]
+        col = hdr_summary.charge_capacity
 
     else:
         col = hdr_summary[col_name]
@@ -344,8 +346,8 @@ def remove_outliers_from_summary_on_nn_distance(
     """
     if filter_cols is None:
         filter_cols = [
-            hdr_summary["charge_capacity"],
-            hdr_summary["discharge_capacity"],
+            hdr_summary.charge_capacity,
+            hdr_summary.discharge_capacity,
         ]
 
     def neighbour_window(y):
@@ -391,8 +393,8 @@ def remove_outliers_from_summary_on_zscore(
 
     if filter_cols is None:
         filter_cols = [
-            hdr_summary["charge_capacity"],
-            hdr_summary["discharge_capacity"],
+            hdr_summary.charge_capacity,
+            hdr_summary.discharge_capacity,
         ]
 
     s2 = s[filter_cols].copy()
@@ -424,8 +426,8 @@ def remove_outliers_from_summary_on_value(
     """
     if filter_cols is None:
         filter_cols = [
-            hdr_summary["charge_capacity"],
-            hdr_summary["discharge_capacity"],
+            hdr_summary.charge_capacity,
+            hdr_summary.discharge_capacity,
         ]
 
     s2 = s[filter_cols].copy()
@@ -756,7 +758,7 @@ def concatenate_summaries(
         group_nest.append(b.pages.group.to_list())
 
     default_columns = [hdr_summary["charge_capacity_gravimetric"]]
-    hdr_norm_cycle = hdr_summary["normalized_cycle_index"]
+    hdr_norm_cycle = hdr_summary.normalized_cycle_index
 
     if columns is None:
         columns = []
@@ -786,16 +788,16 @@ def concatenate_summaries(
 
     if normalize_capacity_on is not None:
         normalize_capacity_headers = [
-            hdr_summary["normalized_charge_capacity"],
-            hdr_summary["normalized_discharge_capacity"],
+            hdr_summary.normalized_charge_capacity,
+            hdr_summary.normalized_discharge_capacity,
         ]
         output_columns = [
             col
             for col in output_columns
             if col
             not in [
-                hdr_summary["charge_capacity"],
-                hdr_summary["discharge_capacity"],
+                hdr_summary.charge_capacity,
+                hdr_summary.discharge_capacity,
             ]
         ]
         output_columns.extend(normalize_capacity_headers)
@@ -917,7 +919,7 @@ def _partition_summary_based_on_cv_steps(
     import pandas as pd
 
     if not x:
-        x = hdr_summary["cycle_index"]
+        x = hdr_summary.cycle_index
 
     summary = c.data.summary.copy()
 
@@ -1081,7 +1083,7 @@ def concat_summaries(
         group_nest.append(pages.group.to_list())
 
     default_columns = [hdr_summary["charge_capacity_gravimetric"]]
-    hdr_norm_cycle = hdr_summary["normalized_cycle_index"]
+    hdr_norm_cycle = hdr_summary.normalized_cycle_index
 
     if columns is None:
         columns = []
@@ -1111,16 +1113,16 @@ def concat_summaries(
 
     if normalize_capacity_on is not None:
         normalize_capacity_headers = [
-            hdr_summary["normalized_charge_capacity"],
-            hdr_summary["normalized_discharge_capacity"],
+            hdr_summary.normalized_charge_capacity,
+            hdr_summary.normalized_discharge_capacity,
         ]
         output_columns = [
             col
             for col in output_columns
             if col
             not in [
-                hdr_summary["charge_capacity"],
-                hdr_summary["discharge_capacity"],
+                hdr_summary.charge_capacity,
+                hdr_summary.discharge_capacity,
             ]
         ]
         output_columns.extend(normalize_capacity_headers)
@@ -1456,16 +1458,16 @@ def select_summary_based_on_rate(
         filtered summary (Pandas.DataFrame).
     """
     if on is None:
-        on = ["charge"]
+        on = [StepType.CHARGE.value]
     else:
         if not isinstance(on, (list, tuple)):
             on = [on]
 
     if rate_column is None:
-        rate_column = hdr_steps["rate_avr"]
+        rate_column = hdr_steps.rate_avr
 
     if on:
-        on_column = hdr_steps["type"]
+        on_column = hdr_steps.type
 
     if rate is None:
         rate = 0.05
@@ -1473,7 +1475,7 @@ def select_summary_based_on_rate(
     if rate_std is None:
         rate_std = 0.1 * rate
 
-    cycle_number_header = hdr_summary["cycle_index"]
+    cycle_number_header = hdr_summary.cycle_index
 
     step_table = cell.data.steps
 
@@ -1545,10 +1547,10 @@ def add_normalized_capacity(
     if norm_cycles is None:
         norm_cycles = [1, 2, 3, 4, 5]
 
-    col_name_charge = hdr_summary["charge_capacity"]
-    col_name_discharge = hdr_summary["discharge_capacity"]
-    col_name_norm_charge = hdr_summary["normalized_charge_capacity"]
-    col_name_norm_discharge = hdr_summary["normalized_discharge_capacity"]
+    col_name_charge = hdr_summary.charge_capacity
+    col_name_discharge = hdr_summary.discharge_capacity
+    col_name_norm_charge = hdr_summary.normalized_charge_capacity
+    col_name_norm_discharge = hdr_summary.normalized_discharge_capacity
 
     try:
         norm_val_charge = cell.data.summary.loc[norm_cycles, col_name_charge].mean()

{cellpy-2.0.0a2 → cellpy-2.0.0a3}/cellpy/utils/ocv_rlx.py

@@ -18,6 +18,8 @@ import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 
+from cellpycore.config import StepType
+
 from cellpy import cellreader
 from cellpy.parameters.internal_settings import get_headers_normal, get_headers_step_table
 
@@ -371,21 +373,21 @@ class MultiCycleOcvFit:
         if direction == "up":
             end_voltage = step_table[
                 (step_table[hdr_steps.cycle] == cycle)
-                & (step_table[hdr_steps.type].isin(["discharge"]))
+                & (step_table[hdr_steps.type].isin([StepType.DISCHARGE.value]))
             ][hdr.voltage + "_last"].values[0]
 
             end_current = step_table[
                 (step_table[hdr_steps.cycle] == cycle)
-                & (step_table[hdr_steps.type].isin(["discharge"]))
+                & (step_table[hdr_steps.type].isin([StepType.DISCHARGE.value]))
             ][hdr.current + "_last"].values[0]
 
         elif direction == "down":
             end_voltage = step_table[
-                (step_table[hdr_steps.cycle] == cycle) & (step_table[hdr_steps.type].isin(["charge"]))
+                (step_table[hdr_steps.cycle] == cycle) & (step_table[hdr_steps.type].isin([StepType.CHARGE.value]))
             ][hdr.voltage + "_last"].values[0]
 
             end_current = step_table[
-                (step_table[hdr_steps.cycle] == cycle) & (step_table[hdr_steps.type].isin(["charge"]))
+                (step_table[hdr_steps.cycle] == cycle) & (step_table[hdr_steps.type].isin([StepType.CHARGE.value]))
             ][hdr.current + "_last"].values[0]
 
         return end_current, end_voltage