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eleanorfrajka merged 6 commits into from
Aug 14, 2026
Merged

[REFACTOR] Report templates to files + unify chrome via base.html #74

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27e97f0
refactor: extract report page templates to files loaded via FileSyste…
eleanorfrajka Aug 13, 2026
ed076aa
refactor: unify report chrome into base.html with per-page accents
eleanorfrajka Aug 13, 2026
5280966
refactor: factor report masthead into base.html; add wordmark
eleanorfrajka Aug 14, 2026
3a167eb
test: fixture for array
eleanorfrajka Aug 14, 2026
a797ae9
refactor: address review — recovery_table white masthead, configurabl…
eleanorfrajka Aug 14, 2026
eb469c8
fix: normalise conductivity to mS/cm on read; refresh stale S/m fixtures
eleanorfrajka Aug 14, 2026
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5 changes: 5 additions & 0 deletions oceanarray/config/parameters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,11 @@

import numpy as np

# ---------------------------------------------------------------------------
# Package identity (shown as the report masthead wordmark)
# ---------------------------------------------------------------------------
PACKAGE_NAME = "oceanarray"

# ---------------------------------------------------------------------------
# Matplotlib style path (used by plotters via plt.style.use)
# ---------------------------------------------------------------------------
Expand Down
29 changes: 28 additions & 1 deletion oceanarray/processors/stage1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -845,8 +845,22 @@ def _iso_date(raw: str) -> str:

return dataset

#: Unit strings (lower-cased) that denote conductivity in S/m. A conductivity
#: variable carrying any of these is converted to the project's canonical
#: mS/cm (1 S/m = 10 mS/cm).
_SM_CONDUCTIVITY_UNITS = frozenset(
{"s/m", "s m-1", "sm-1", "s.m-1", "siemens/meter", "siemens per metre"}
)

def _normalize_conductivity(self, dataset: xr.Dataset) -> xr.Dataset:
"""Convert conductivity to mS/cm and rename to 'conductivity' if needed."""
"""Normalise conductivity to the canonical mS/cm and rename it if needed.

Handles the raw SBE CNV column names ``cond0S/m`` / ``cond0mS/cm`` and,
for inputs that already provide a ``conductivity`` variable, converts it
from S/m to mS/cm when its ``units`` attribute says so (1 S/m = 10 mS/cm).
The source unit is recorded in ``conductivity_normalised_from`` so the
treatment can be reconstructed from the output file alone.
"""
if "cond0S/m" in dataset:
# S/m → mS/cm: multiply by 10
data = dataset["cond0S/m"] * 10.0
Expand All @@ -856,6 +870,19 @@ def _normalize_conductivity(self, dataset: xr.Dataset) -> xr.Dataset:
dataset["conductivity"] = data
elif "cond0mS/cm" in dataset:
dataset = dataset.rename({"cond0mS/cm": "conductivity"})

# An input already named 'conductivity' but reported in S/m (e.g. an
# older seasenselib release) → convert to the canonical mS/cm.
if "conductivity" in dataset:
src_units = str(dataset["conductivity"].attrs.get("units", "")).strip()
if src_units.lower() in self._SM_CONDUCTIVITY_UNITS:
data = dataset["conductivity"] * 10.0
data.attrs = dict(dataset["conductivity"].attrs)
data.attrs["units"] = "mS cm-1"
data.attrs["conductivity_normalised_from"] = (
f"{src_units} (x10 to mS cm-1)"
)
dataset["conductivity"] = data
return dataset

# Known SBE CNV variable names containing '/' and their CF-compatible replacements.
Expand Down
185 changes: 2 additions & 183 deletions oceanarray/reports/_array.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@

import numpy as np

from ._env import render_template
from ._html_helpers import (
_duration_str,
_parse_dt,
Expand Down Expand Up @@ -147,185 +148,6 @@ def _draw() -> "plt.Figure":
return render_b64(_draw, optional=True)


# ---------------------------------------------------------------------------
# HTML template
# ---------------------------------------------------------------------------

_ARRAY_HTML_TEMPLATE = """\
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Array report &ndash; {{ array_name }}</title>
<style>
:root { --ocean:#1a3a5c; --seafoam:#e8f4f8; --text:#2c3e50; --muted:#95a5a6; }
body { font-family: system-ui, sans-serif; max-width: 1100px; margin: 0 auto; padding: 1rem; color: var(--text); }
.masthead { background: var(--ocean); color:#fff; border-radius:6px; padding:1.2rem 1.6rem 1rem; margin-bottom:1.2rem; }
.masthead h1 { margin:0 0 0.2rem; font-size:1.6rem; }
.masthead p.sub { margin:0; font-size:0.82rem; opacity:0.75; }
.meta-grid { display:flex; flex-wrap:wrap; gap:0.5rem 1.4rem; margin-top:0.8rem; }
.meta-grid div { font-size:0.82rem; }
.meta-grid dt { opacity:0.7; font-size:0.72rem; }
.meta-grid dd { margin:0; font-weight:600; }
.meta-miss dd { color:#f0ad4e; }
table { border-collapse:collapse; width:100%; margin:0.6rem 0 1.2rem; font-size:0.84rem; }
th { background:var(--ocean); color:#fff; padding:0.4rem 0.6rem; text-align:left; }
td { padding:0.35rem 0.6rem; border-bottom:1px solid #e8ecef; }
tr:nth-child(even) td { background:#f7f9fb; }
.num { text-align:right; }
.btn { display:inline-block; padding:0.15em 0.55em; border-radius:4px; font-size:0.75rem;
font-weight:700; text-decoration:none; color:#fff; margin:0 0.15rem 0.2rem 0; }
.btn-sum { background:#2c3e50; }
.btn-stk { background:#2980b9; }
.btn-grd { background:#8e44ad; }
.btn-miss { background:#bbb; cursor:default; pointer-events:none; }
.note { font-size:0.78rem; color:#555; margin:0.2rem 0 0.6rem; }
.fig { max-width:60%; display:block; margin:0.5rem auto 1rem; border:1px solid #e0e4e8; border-radius:4px; }
h2 { color:var(--ocean); border-bottom:2px solid var(--seafoam); padding-bottom:0.3rem; margin-top:1.4rem; }
</style>
</head>
<body>

<div class="masthead">
<h1>{{ array_name }}</h1>
<p class="sub">Array summary &bull; generated {{ generated }}</p>
<dl class="meta-grid">
{% if year %}<div><dt>Year</dt><dd>{{ year }}</dd></div>{% endif %}
{% if cruise %}<div><dt>Cruise</dt><dd>{{ cruise }}</dd></div>{% endif %}
{% if ship %}<div><dt>Ship</dt><dd>{{ ship }}</dd></div>{% endif %}
{% if project %}<div><dt>Project</dt><dd>{{ project }}</dd></div>{% endif %}
{% if deploy_time %}<div><dt>Deployment</dt><dd>{{ deploy_time }}</dd></div>{% endif %}
{% if recover_time %}<div><dt>Recovery</dt><dd>{{ recover_time }}</dd></div>{% endif %}
<div><dt>Moorings</dt><dd>{{ moorings | length }}</dd></div>
</dl>
</div>

<p class="note" style="margin:0 0 0.8rem">
Jump to:
<a href="#moorings">Moorings</a> &bull;
<a href="#type-summary">Instrument summary</a> &bull;
<a href="#completeness">Completeness</a>
</p>

{% if fig_map_b64 %}
<h2>Mooring positions</h2>
<img class="fig" src="data:image/png;base64,{{ fig_map_b64 }}" alt="Array map">
{% endif %}

<h2 id="moorings">Moorings</h2>
<table>
<thead>
<tr>
<th>#</th>
<th>Mooring</th>
<th class="num">Latitude</th>
<th class="num">Longitude</th>
<th class="num">Depth&nbsp;(m)</th>
<th>Deployment</th>
<th>Recovery</th>
<th class="num">Duration</th>
<th class="num">Instruments</th>
<th>Reports</th>
</tr>
</thead>
<tbody>
{% for r in moorings %}
<tr>
<td class="num">{% if r.color_hex %}<span style="display:inline-block;width:0.75em;height:0.75em;border-radius:50%;background:{{ r.color_hex }};margin-right:0.35em;vertical-align:middle"></span>{% endif %}{{ r.position }}</td>
<td><strong>{{ r.mooring }}</strong></td>
<td class="num">{{ "%.4f"|format(r.lat) if r.lat is not none else "—" }}</td>
<td class="num">{{ "%.4f"|format(r.lon) if r.lon is not none else "—" }}</td>
<td class="num">{{ r.waterdepth if r.waterdepth else "—" }}</td>
<td>{{ r.deploy_time }}</td>
<td>{{ r.recover_time }}</td>
<td class="num">{{ r.duration }}</td>
<td class="num">{{ r.n_instruments }}</td>
<td>
{% if r.report_exists %}
<a class="btn btn-sum" href="{{ r.report_href }}">Summary</a>
{% else %}
<span class="btn btn-miss">Summary</span>
{% endif %}
{% if r.stack_exists %}
<a class="btn btn-stk" href="{{ r.stack_href }}">Stack</a>
{% endif %}
{% if r.grid_exists %}
<a class="btn btn-grd" href="{{ r.grid_href }}">Grid</a>
{% endif %}
</td>
</tr>
{% endfor %}
</tbody>
</table>

{% if type_summary %}
<h2 id="type-summary">Instrument type summary</h2>
<table>
<thead>
<tr>
<th>Type</th>
<th class="num">Deployed</th>
<th class="num">Complete&nbsp;(Stage&nbsp;3&nbsp;✓)</th>
<th class="num">Skipped&nbsp;/&nbsp;no&nbsp;raw</th>
<th class="num">Stopped&nbsp;early</th>
<th>Notes</th>
</tr>
</thead>
<tbody>
{% for row in type_summary %}
<tr>
<td>{{ row.itype }}</td>
<td class="num">{{ row.deployed }}</td>
<td class="num">{{ row.complete }}</td>
<td class="num">{{ row.skipped }}</td>
<td class="num">{{ row.stopped_early }}</td>
<td>{{ row.notes }}</td>
</tr>
{% endfor %}
</tbody>
</table>
{% endif %}

{% if mooring_completeness %}
<h2 id="completeness">Data completeness by mooring</h2>
<table>
<thead>
<tr>
<th>Mooring</th>
<th class="num">Depth&nbsp;(m)</th>
<th class="num">Deployed</th>
<th class="num">Complete</th>
<th class="num">Skipped</th>
<th class="num">Stopped&nbsp;early</th>
<th>Deployment&nbsp;(UTC)</th>
<th>Recovery&nbsp;(UTC)</th>
<th class="num">Duration</th>
</tr>
</thead>
<tbody>
{% for row in mooring_completeness %}
<tr>
<td><strong>{{ row.mooring }}</strong></td>
<td class="num">{{ row.waterdepth if row.waterdepth else "—" }}</td>
<td class="num">{{ row.deployed }}</td>
<td class="num">{{ row.complete }}</td>
<td class="num">{{ row.skipped }}</td>
<td class="num">{{ row.stopped_early }}</td>
<td>{{ row.deploy_time }}</td>
<td>{{ row.recover_time }}</td>
<td class="num">{{ row.duration }}</td>
</tr>
{% endfor %}
</tbody>
</table>
{% endif %}

</body>
</html>
"""


# ---------------------------------------------------------------------------
# Instrument status helpers
# ---------------------------------------------------------------------------
Expand Down Expand Up @@ -522,8 +344,6 @@ def generate_array_report(
"""
from datetime import datetime, timezone

from jinja2 import Environment

array_yaml_path = Path(array_yaml_path)
proc_dir = Path(proc_dir)

Expand Down Expand Up @@ -655,8 +475,7 @@ def generate_array_report(
"generated": datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M UTC"),
}

env = Environment(autoescape=True)
html = env.from_string(_ARRAY_HTML_TEMPLATE).render(**ctx)
html = render_template("array.html", **ctx)
out_path.write_text(html, encoding="utf-8")
_status("file", str(out_path))
return out_path
51 changes: 51 additions & 0 deletions oceanarray/reports/_env.py
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@@ -0,0 +1,51 @@
"""File-based Jinja environment for the report HTML templates.

Report page templates live in ``reports/templates/`` and are loaded with a
:class:`~jinja2.FileSystemLoader` so they can use ``{% extends %}`` and
``{% include %}`` — which the previous inline template strings could not.

The environment settings are byte-identical to the previous per-module
``Environment(autoescape=True)`` calls (autoescape on; ``trim_blocks`` and
``lstrip_blocks`` at Jinja's defaults of ``False``), so migrating a template
from an inline string to a file does not change the rendered output.
"""

from __future__ import annotations

from pathlib import Path
from typing import Any

from jinja2 import Environment, FileSystemLoader

from .. import parameters as params

#: Directory holding the report page templates.
TEMPLATES_DIR: Path = Path(__file__).with_name("templates")

_ENV = Environment(
loader=FileSystemLoader(str(TEMPLATES_DIR)),
autoescape=True,
auto_reload=False,
)
#: Package identity available to every template (masthead wordmark).
_ENV.globals["package_name"] = params.PACKAGE_NAME


def render_template(name: str, /, **context: Any) -> str:
"""Render report template *name* with *context* and return the HTML string.

Parameters
----------
name : str
Template filename relative to ``reports/templates/`` (e.g.
``"instrument.html"``).
**context
Template variables, forwarded to :meth:`jinja2.Template.render`.

Returns
-------
str
The rendered HTML.

"""
return _ENV.get_template(name).render(**context)
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