Hapi csv codec by RichardHitier · Pull Request #277 · SciQLop/speasy

RichardHitier · 2026-03-02T17:40:52Z

Enhance hapi csv codec features: read mulitaxis variables, and write speasy to hapi csv.

codecov · 2026-03-03T12:47:19Z

Codecov Report

❌ Patch coverage is 83.75000% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.48%. Comparing base (92d5bec) to head (36f946d).
⚠️ Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
...peasy/core/codecs/bundled_codecs/hapi_csv/codec.py	81.53%	8 Missing and 4 partials ⚠️
...easy/core/codecs/bundled_codecs/hapi_csv/writer.py	93.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #277      +/-   ##
==========================================
+ Coverage   84.34%   84.48%   +0.14%     
==========================================
  Files          69       69              
  Lines        4771     4834      +63     
  Branches      656      668      +12     
==========================================
+ Hits         4024     4084      +60     
+ Misses        516      508       -8     
- Partials      231      242      +11

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jeandet · 2026-03-11T11:11:36Z

tests/test_hapi_codecs.py

+    def test_spz_getdata_to_csv(self):
+        hapi_csv_codec: CodecInterface = get_codec('hapi/csv')
+        spz_var = spz.get_data("cda/STA_L1_HET/Proton_Flux", "2020-10-28", "2020-10-28T01")
+        hapi_csv_file = hapi_csv_codec.save_variables(variables=[spz_var], file='test_output.csv')


Use tmp file or dir for auto cleanup.

jeandet · 2026-03-11T11:14:26Z

speasy/core/codecs/bundled_codecs/hapi_csv/codec.py

        raise ValueError("No variables to save")
    hapi_csv_file = HapiCsvFile()
-    hapi_csv_file.add_parameter(_make_hapi_csv_time_axis(variables[0].time))
+    hapi_csv_file.add_parameter(_make_hapi_csv_time_axis(variables[0].axes[0]))


time is cleaner and show the intent

jeandet · 2026-03-11T11:16:13Z

speasy/core/codecs/bundled_codecs/hapi_csv/codec.py

+    for ax in _get_variable_axes(variable, is_time_dependent=True):
+        meta = {
+            "name": _time_dependent_axis_name(ax),
+            "type": "double",


Not sure hard-coding the type here is safe, ax.values can be of any numerical type.

done (refactored with _create_meta())

jeandet · 2026-03-11T11:21:12Z

speasy/core/codecs/bundled_codecs/hapi_csv/writer.py

+        json_str = json.dumps(headers, indent=2, ensure_ascii=False)
+        commented = "\n".join("#" + line for line in json_str.splitlines())
+        dest.write((commented + "\n").encode("utf-8"))


Why do we need this?

this is how we prepend the json headers as comment on top of .csv file

Sure but why binary and multi-lines?

multilines because I find it more human readable

binary because it was the orginal format sent by save_hapi_csv()

do you prefer

one-line header ?

change save_hapi_csv() for a text data type ?

one line is faster so yes for this one.
For text, I don't know, it was just suspicious we had to do this, I want to be sure we do not miss anything that would break later.

jeandet · 2026-03-11T11:27:07Z

speasy/core/codecs/bundled_codecs/hapi_csv/codec.py

+    time_dependent_axes = _get_variable_axes(variable, is_time_dependent=True)
+    if time_dependent_axes:
+        bins.extend([
+            {"name": ax.name, "unit": ax.unit, "centers": _time_dependent_axis_name(ax)}


Suggested change

{"name": ax.name, "unit": ax.unit, "centers": _time_dependent_axis_name(ax)}

{"name": ax.name, "units": ax.unit, "centers": _time_dependent_axis_name(ax)}

jeandet · 2026-03-11T11:27:43Z

tests/test_hapi_codecs.py

+            variables = hapi_csv_codec.load_variables(file=f, variables=['spectra_time_dependent_bins'], disable_cache=True)
+            self.assertIn('spectra_time_dependent_bins', variables)
+
+    def test_load_time_independant_axis(self):


Suggested change

def test_load_time_independant_axis(self):

def test_load_time_independent_axis(self):

Copilot

Pull request overview

Enhances the HAPI CSV codec to better support multi-axis (binned) variables on read and to export Speasy variables to HAPI CSV, with added regression tests and new CSV fixtures.

Changes:

Add tests and fixtures for time-independent and time-varying bin axes in HAPI CSV.
Extend HAPI CSV codec to decode bins into VariableAxis objects and emit bins metadata when saving.
Update HAPI CSV writer to output pretty-printed commented JSON headers and to expand multi-dimensional values into CSV columns.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
tests/test_hapi_codecs.py	Adds unit tests for bin-axis decoding and for saving variables back to HAPI CSV.
tests/resources/HAPI_ndData_TimeVarying_Axis.csv	New fixture covering time-varying bin centers/ranges.
tests/resources/HAPI_ndData_TimeIndependent_Axis.csv	New fixture covering time-independent bin centers/ranges.
speasy/core/codecs/bundled_codecs/hapi_csv/writer.py	Updates header serialization and flattens multi-dim parameters into multiple CSV columns.
speasy/core/codecs/bundled_codecs/hapi_csv/codec.py	Adds bins<->axes mapping for load/save and writes additional parameters for time-varying axes.

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Copilot · 2026-03-11T11:35:18Z

speasy/core/codecs/bundled_codecs/hapi_csv/writer.py

+        json_str = json.dumps(headers, indent=2, ensure_ascii=False)
+        commented = "\n".join("#" + line for line in json_str.splitlines())
+        dest.write((commented + "\n").encode("utf-8"))


The header is written as bytes (encode('utf-8')) but pandas.DataFrame.to_csv typically writes strings to the same dest. If dest is a text stream, line 21 will raise TypeError; if dest is a binary stream, to_csv may fail when writing strings. Use a consistent text writer for both header and dataframe output (e.g., write commented + '\\n' as str, or wrap a binary stream with a TextIOWrapper and pass that same wrapper to both writes).

Copilot · 2026-03-11T11:35:19Z

speasy/core/codecs/bundled_codecs/hapi_csv/writer.py

    df = pds.DataFrame(data)
    df.to_csv(dest, index=False, header=False, date_format='%Y-%m-%dT%H:%M:%S.%fZ', float_format='%.3g')


The header is written as bytes (encode('utf-8')) but pandas.DataFrame.to_csv typically writes strings to the same dest. If dest is a text stream, line 21 will raise TypeError; if dest is a binary stream, to_csv may fail when writing strings. Use a consistent text writer for both header and dataframe output (e.g., write commented + '\\n' as str, or wrap a binary stream with a TextIOWrapper and pass that same wrapper to both writes).

Copilot · 2026-03-11T11:35:19Z

speasy/core/codecs/bundled_codecs/hapi_csv/writer.py

+        vals = param.values
+        if vals.ndim == 1:
+            data[param.name] = vals
+        else:
+            for i in range(vals.shape[1]):
+                data[f"{param.name}_{i}"] = vals[:, i]


Multi-dimensional values are only expanded along shape[1] and sliced with vals[:, i]. For ndim > 2, vals[:, i] remains multi-dimensional and will produce object-like columns or inconsistent CSV output. Consider reshaping values to 2D (time, -1) and generating column names for all flattened components (or iterating across all non-time indices) so ndData variables with >2 dimensions serialize predictably.

Copilot · 2026-03-11T11:35:19Z

speasy/core/codecs/bundled_codecs/hapi_csv/codec.py

+            {"name": ax.name, "unit": ax.unit, "centers": ax.values.tolist()}
+            for ax in time_independent_axes
+        ])
+
+    time_dependent_axes = _get_variable_axes(variable, is_time_dependent=True)
+    if time_dependent_axes:
+        bins.extend([
+            {"name": ax.name, "unit": ax.unit, "centers": _time_dependent_axis_name(ax)}


The bin metadata uses the key unit, but HAPI parameter metadata (and your fixtures) use units. This will cause _decode_meta / _bin_to_axis to miss units and drop axis units on load. Rename unit to units in the created bins entries to match the HAPI schema and the rest of the codec.

Suggested change

{"name": ax.name, "unit": ax.unit, "centers": ax.values.tolist()}

for ax in time_independent_axes

])

time_dependent_axes = _get_variable_axes(variable, is_time_dependent=True)

if time_dependent_axes:

bins.extend([

{"name": ax.name, "unit": ax.unit, "centers": _time_dependent_axis_name(ax)}

{"name": ax.name, "units": ax.unit, "centers": ax.values.tolist()}

for ax in time_independent_axes

])

time_dependent_axes = _get_variable_axes(variable, is_time_dependent=True)

if time_dependent_axes:

bins.extend([

{"name": ax.name, "units": ax.unit, "centers": _time_dependent_axis_name(ax)}

Copilot · 2026-03-11T11:35:19Z

speasy/core/codecs/bundled_codecs/hapi_csv/codec.py

+            {"name": ax.name, "unit": ax.unit, "centers": ax.values.tolist()}
+            for ax in time_independent_axes
+        ])
+
+    time_dependent_axes = _get_variable_axes(variable, is_time_dependent=True)
+    if time_dependent_axes:
+        bins.extend([
+            {"name": ax.name, "unit": ax.unit, "centers": _time_dependent_axis_name(ax)}


The bin metadata uses the key unit, but HAPI parameter metadata (and your fixtures) use units. This will cause _decode_meta / _bin_to_axis to miss units and drop axis units on load. Rename unit to units in the created bins entries to match the HAPI schema and the rest of the codec.

Suggested change

{"name": ax.name, "unit": ax.unit, "centers": ax.values.tolist()}

for ax in time_independent_axes

])

time_dependent_axes = _get_variable_axes(variable, is_time_dependent=True)

if time_dependent_axes:

bins.extend([

{"name": ax.name, "unit": ax.unit, "centers": _time_dependent_axis_name(ax)}

{"name": ax.name, "units": ax.unit, "centers": ax.values.tolist()}

for ax in time_independent_axes

])

time_dependent_axes = _get_variable_axes(variable, is_time_dependent=True)

if time_dependent_axes:

bins.extend([

{"name": ax.name, "units": ax.unit, "centers": _time_dependent_axis_name(ax)}

Copilot · 2026-03-11T11:35:20Z

speasy/core/codecs/bundled_codecs/hapi_csv/codec.py

+def _bin_to_axis(json_bin: Dict[str, Any], hap_csv_file: HapiCsvFile) -> VariableAxis:
+    centers = json_bin.get("centers")
+    name = json_bin.get("name", "bin_axis")
+    if centers is None:
+        raise ValueError("Invalid bin specification: missing 'centers' field")
+    if isinstance(centers, str):
+        hapi_parameter = hap_csv_file.get_parameter(centers)


Parameter name hap_csv_file looks like a typo and is easy to confuse with hapi_csv_file used elsewhere. Renaming it to hapi_csv_file would improve readability and reduce the chance of mistakes when editing these helpers.

Suggested change

def _bin_to_axis(json_bin: Dict[str, Any], hap_csv_file: HapiCsvFile) -> VariableAxis:

centers = json_bin.get("centers")

name = json_bin.get("name", "bin_axis")

if centers is None:

raise ValueError("Invalid bin specification: missing 'centers' field")

if isinstance(centers, str):

hapi_parameter = hap_csv_file.get_parameter(centers)

def _bin_to_axis(json_bin: Dict[str, Any], hapi_csv_file: HapiCsvFile) -> VariableAxis:

centers = json_bin.get("centers")

name = json_bin.get("name", "bin_axis")

if centers is None:

raise ValueError("Invalid bin specification: missing 'centers' field")

if isinstance(centers, str):

hapi_parameter = hapi_csv_file.get_parameter(centers)

Copilot · 2026-03-11T11:35:21Z

speasy/core/codecs/bundled_codecs/hapi_csv/codec.py

+    return variable_axis
+
+
+def _bins_to_axes(json_bins: List[Dict[str, Any]], hap_csv_file: HapiCsvFile) -> List[VariableAxis]:


Parameter name hap_csv_file looks like a typo and is easy to confuse with hapi_csv_file used elsewhere. Renaming it to hapi_csv_file would improve readability and reduce the chance of mistakes when editing these helpers.

Copilot · 2026-03-11T11:35:21Z

tests/test_hapi_codecs.py

+    def test_spz_getdata_to_csv(self):
+        hapi_csv_codec: CodecInterface = get_codec('hapi/csv')
+        spz_var = spz.get_data("cda/STA_L1_HET/Proton_Flux", "2020-10-28", "2020-10-28T01")
+        hapi_csv_file = hapi_csv_codec.save_variables(variables=[spz_var], file='test_output.csv')
+        self.assertTrue(hapi_csv_file)


This test performs a live spz.get_data(...) call (network / remote dependency) and writes to a fixed path (test_output.csv) in the working directory, which can make CI flaky and pollute the repo. Consider converting this into an integration test (skipped by default), mocking spz.get_data, and writing to a NamedTemporaryFile similar to the other save tests.

Copilot · 2026-03-11T11:35:21Z

tests/test_hapi_codecs.py

+            variables = hapi_csv_codec.load_variables(file=f, variables=['spectra_time_dependent_bins'], disable_cache=True)
+            self.assertIn('spectra_time_dependent_bins', variables)
+
+    def test_load_time_independant_axis(self):


Correct spelling: 'independant' -> 'independent' in the test name.

Suggested change

def test_load_time_independant_axis(self):

def test_load_time_independent_axis(self):

Copilot · 2026-03-11T11:35:21Z

tests/resources/HAPI_ndData_TimeVarying_Axis.csv

+#}
+
+1970-01-01T00:00:00.000Z,0,1,0.5,0.3333333333333333,0.25,0.2,0.16666666666666666,0.14285714285714285,0.125,0.1111111111111111,11,13,15,17,19,21,23,25,27,29,10,12,12,14,14,16,16,18,18,20,20,22,22,24,24,26,26,28,28,30
+1970-01-01T00:01:08.000Z,0,1,0.5,0.3333333333333333,0.25,0.2,0.16666666666666666,0.14285714285714285,0.125,0.1111111111111111,1,3,5,7,9,11,13,15,17,19


The header declares three parameters after Time: spectra_time_dependent_bins (10 values), frequency_centers_time_varying (10 values), and frequency_ranges_time_varying (10x2 = 20 values). Row 68 includes the additional 20 range values, but row 69 does not, so the CSV row length is inconsistent with the declared schema. Update row 69 to include the missing 20 values (or remove/adjust the declared ranges parameter) so the fixture can be parsed reliably.

Suggested change

1970-01-01T00:01:08.000Z,0,1,0.5,0.3333333333333333,0.25,0.2,0.16666666666666666,0.14285714285714285,0.125,0.1111111111111111,1,3,5,7,9,11,13,15,17,19

1970-01-01T00:01:08.000Z,0,1,0.5,0.3333333333333333,0.25,0.2,0.16666666666666666,0.14285714285714285,0.125,0.1111111111111111,1,3,5,7,9,11,13,15,17,19,0,2,2,4,4,6,6,8,8,10,10,12,12,14,14,16,16,18,18,20

brenard-irap · 2026-03-13T10:30:00Z

Thank you, Richard.

A few remarks that could be discussed.

Here is what I am doing:

import speasy as spz
imf_data = spz.get_data(spz.inventories.tree.amda.Parameters.ACE.MFI.ace_imf_all.imf, "2008-01-01", "2008-01-02")
hapi_csv_codec = spz.core.codecs.get_codec('hapi/csv')
hapi_csv_codec.save_variables(variables=[imf_data], file='./imf_data_hapi.csv')

1. Missing required fields in the header

Currently, we have the following header:

#{
#  "HAPI": "3.2",
#  "status": {
#    "code": 1200,
#    "message": "OK request successful"
#  },
#  "parameters": [
#    {
#      "name": "Time",
#      "type": "isotime",
#      "units": "UTC",
#      "length": 30,
#      "fill": null
#    },
#    {
#      "name": "imf",
#      "units": "nT",
#      "fill": [
#        NaN
#      ],
#      "description": "",
#      "type": "double",
#      "label": [
#        "bx",
#        "by",
#        "bz"
#      ],
#      "size": [
#        3
#      ]
#    }
#  ]
#}

In my view, the writer should directly produce an output that complies with the HAPI specification: https://github.com/hapi-server/data-specification/blob/master/hapi-3.2.0/HAPI-data-access-spec-3.2.0.md#372-response

As stated in the spec, “the contents of the header should be the same as returned from the info endpoint.”

Based on this, I would expect the header to include at least the required fields listed here: https://github.com/hapi-server/data-specification/blob/master/hapi-3.2.0/HAPI-data-access-spec-3.2.0.md#362-info-response-object

In the current response, the following fields are missing:

format: for the hapi/csv writer this should be "csv"
startDate: could default to the first time in the variable
stopDate: could default to the last time in the variable

2. Data precision in the written file

The first data row in the generated CSV file is:

2008-01-01T00:00:08.000000Z,-3.84,0.428,-1.9

However, when inspecting the first data point directly in Python, I get:

>>> imf_data.values[0]
array([-3.84 ,  0.428, -1.905], dtype=float32)

There is a noticeable loss of precision on the third component.
After checking, this comes from the float_format definition in the writer:
https://github.com/co-libri-org/speasy/blob/6e920569ae0172cf7f967b281ff1b74e4e364c5b/speasy/core/codecs/bundled_codecs/hapi_csv/writer.py#L34

3. Optional header

Since the "data" endpoint allows the header to be optional, it would be useful to add a writer option to enable or disable header generation.
This would make the writer more flexible and aligned with the endpoint’s behavior.

I’ll continue running some additional tests on my side.

brenard-irap · 2026-03-12T15:09:18Z

speasy/core/codecs/bundled_codecs/hapi_csv/codec.py

+    elif np.issubdtype(dtype, np.floating):
+        return "double"
+    else:
+        raise ValueError(f"Unsupported data type {variable.values.dtype}")


variable is not defined

yes, sorry.
I have my own flake8 settings on pre-commit now ;-)

tests/test_hapi_codecs.py

@@ -1,10 +1,17 @@
+from datetime import datetime


HAPI CSV json headers may contain the 'bins' field: Build a VariableAxis, either from parameter name or from given values list.

New _bins_to_axes() method used in _hapi_csv_to_speasy_variable(): if 'bins' in hapi meta, then add as many VariableAxis as there are 'centers' list or variable.

- use temp file in test - use SpzVar.time member - HapiCsvParameter unit to units member - extract SpzVariable dtype

sonarqubecloud · 2026-03-16T17:28:39Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

RichardHitier force-pushed the hapi_csv_codec branch 2 times, most recently from 93da373 to 3c454fe Compare March 3, 2026 11:02

RichardHitier force-pushed the hapi_csv_codec branch 3 times, most recently from c648d39 to ddc0ad1 Compare March 9, 2026 14:05

jeandet reviewed Mar 11, 2026

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jeandet requested review from brenard-irap and Copilot March 11, 2026 11:28

Copilot started reviewing on behalf of jeandet March 11, 2026 11:33 View session

Copilot AI reviewed Mar 11, 2026

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RichardHitier force-pushed the hapi_csv_codec branch 2 times, most recently from 6e92056 to e19a699 Compare March 13, 2026 10:18

brenard-irap reviewed Mar 13, 2026

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RichardHitier force-pushed the hapi_csv_codec branch from e19a699 to 8a9a642 Compare March 13, 2026 14:51

github-advanced-security bot found potential problems Mar 13, 2026

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tests/test_hapi_codecs.py

@@ -1,10 +1,17 @@

from datetime import datetime

Check notice

Code scanning / CodeQL

Unused import Note test

Import of 'datetime' is not used.

RichardHitier force-pushed the hapi_csv_codec branch from 8a9a642 to 36f946d Compare March 13, 2026 15:01

RichardHitier added 12 commits March 16, 2026 18:27

Make variable axis from bins

1f2bc83

HAPI CSV json headers may contain the 'bins' field: Build a VariableAxis, either from parameter name or from given values list.

Allow for multi axes SpeasyVariables

e32b49b

New _bins_to_axes() method used in _hapi_csv_to_speasy_variable(): if 'bins' in hapi meta, then add as many VariableAxis as there are 'centers' list or variable.

Add multi axis variable loading test

b0dc3e2

Test time independent axis

bffe0f0

Fix numpy timezone warning

ddd48b1

Simple writer SpzVar to CSV

35c509a

Indent commented json headers

006bae1

Fix SpeasyVariable name from csv reading

6e1af8d

Add more comprehensive test

a222d1b

Add VariableAxis name at csv loading

20be4e4

Add time independent VariableAxis CSV 'bins'

96de0bb

Add time dependant VariableAxis to CSV

b0debec

RichardHitier added 5 commits March 16, 2026 18:27

Fixes after PR code review

448cfc0

- use temp file in test - use SpzVar.time member - HapiCsvParameter unit to units member - extract SpzVariable dtype

Fix HAPI compliant csv header

71fcda2

Fix float precision in csv writing

7070a50

Allow to save csv without headers

9c1cbb2

Fix HAPI compliant csv header

0919b52

RichardHitier force-pushed the hapi_csv_codec branch from 6f8dc02 to 0919b52 Compare March 16, 2026 17:27

jeandet merged commit 93ce7a0 into SciQLop:main Mar 20, 2026
16 of 23 checks passed

RichardHitier deleted the hapi_csv_codec branch March 23, 2026 13:51

	{"name": ax.name, "unit": ax.unit, "centers": _time_dependent_axis_name(ax)}
	{"name": ax.name, "units": ax.unit, "centers": _time_dependent_axis_name(ax)}

	def test_load_time_independant_axis(self):
	def test_load_time_independent_axis(self):

		df = pds.DataFrame(data)
		df.to_csv(dest, index=False, header=False, date_format='%Y-%m-%dT%H:%M:%S.%fZ', float_format='%.3g')

		return variable_axis


		def _bins_to_axes(json_bins: List[Dict[str, Any]], hap_csv_file: HapiCsvFile) -> List[VariableAxis]:

	1970-01-01T00:01:08.000Z,0,1,0.5,0.3333333333333333,0.25,0.2,0.16666666666666666,0.14285714285714285,0.125,0.1111111111111111,1,3,5,7,9,11,13,15,17,19
	1970-01-01T00:01:08.000Z,0,1,0.5,0.3333333333333333,0.25,0.2,0.16666666666666666,0.14285714285714285,0.125,0.1111111111111111,1,3,5,7,9,11,13,15,17,19,0,2,2,4,4,6,6,8,8,10,10,12,12,14,14,16,16,18,18,20

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Pull request overview

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brenard-irap commented Mar 13, 2026

1. Missing required fields in the header

2. Data precision in the written file

3. Optional header

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codecov bot commented Mar 3, 2026 •

edited

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