jupyter-analysis-tools 1.1.0__tar.gz → 1.2.1__tar.gz

{jupyter_analysis_tools-1.1.0 → jupyter_analysis_tools-1.2.1}/.cookiecutterrc

@@ -20,7 +20,7 @@ default_context:
     release_date:              'today'
     year_from:                 '2018'
     year_to:                   '2023'
-    version:                   '1.1.0'
+    version:                   '1.2.1'
     pypi_host:                 'pypi.org'
     license:                   'MIT license'
     sphinx_theme:              'furo'

{jupyter_analysis_tools-1.1.0 → jupyter_analysis_tools-1.2.1}/CHANGELOG.md

@@ -1,5 +1,41 @@
 # CHANGELOG
 
+## v1.2.1 (2025-07-11)
+
+### Bug fixes
+
+* readme: trigger new version after style changes ([`8b2b5e9`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/8b2b5e93c0f24ae59afaa764abdc508e994946b4))
+
+### Code style
+
+* __init__: imports format ([`6f07790`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/6f07790a04e43736b1c0fbce0eac54d0b661a7cf))
+
+* utils: satisfy flake8 ([`9657474`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/9657474e94a4d9887c4a6b653e0ffa403e666d02))
+
+* readdata: satisfy flake8 ([`36bf6e8`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/36bf6e8be67a2ebd345c5557c2352710bcebed82))
+
+### Continuous integration
+
+* workflow: publish only if the docs are good ([`a663ed3`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/a663ed3d1fd87079a4fd7cf419132a129280a562))
+
+### Testing
+
+* utils: fix imports ([`ddd5369`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/ddd5369b8037f583c6900aea25522a56126c9d32))
+
+## v1.2.0 (2025-07-11)
+
+### Features
+
+* readdata: readSSF() renamed from readSession(), tests added with expected JSON output ([`e2197f6`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/e2197f6bcb032c1bc1a9a7435e024dda763228c4))
+
+* readPDHmeta: routine for reading metadata part from .PDH and .SSF files ([`ea6a1d5`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/ea6a1d554f3763fc05022ae8e4e8909f0993cd43))
+
+### Testing
+
+* readdata: path separator depends on platform ([`1b2866f`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/1b2866f13307c2cf2dedc59f36d7372442ddbfd8))
+
+* readdata: testdata files and testing, using pathlib instead of old os.path ([`aeacfa4`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/aeacfa4a949d7293f2cd3ce5e3004fddf20ecc02))
+
 ## v1.1.0 (2025-07-10)
 
 ### Bug fixes

{jupyter_analysis_tools-1.1.0 → jupyter_analysis_tools-1.2.1}/MANIFEST.in

@@ -17,3 +17,4 @@ include README.rst
 
 global-exclude *.py[cod] __pycache__/* *.so *.dylib .DS_Store */.ipynb_checkpoints/*
 recursive-include templates *.j2
+recursive-include testdata *.pdh *.ssfz *.json

{jupyter_analysis_tools-1.1.0 → jupyter_analysis_tools-1.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: jupyter-analysis-tools
-Version: 1.1.0
+Version: 1.2.1
 Summary: Yet another Python library with helpers and utilities for data analysis and processing.
 Author-email: Ingo Breßler <dev@ingobressler.net>
 License: MIT license
@@ -53,8 +53,8 @@ Yet another Python library with helpers and utilities for data analysis and proc
     :target: https://pypi.org/project/jupyter-analysis-tools
     :alt: PyPI Package latest release
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.1.0.svg
-    :target: https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.1.0...main
+.. |commits-since| image:: https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.2.1.svg
+    :target: https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.2.1...main
     :alt: Commits since latest release
 
 .. |license| image:: https://img.shields.io/pypi/l/jupyter-analysis-tools.svg
@@ -104,9 +104,9 @@ https://BAMresearch.github.io/jupyter-analysis-tools
 Development
 ===========
 
-To run all the tests run::
+Run all tests with::
 
-    tox
+    tox -e py
 
 Note, to combine the coverage data from all the tox environments run:
 
@@ -127,6 +127,42 @@ Note, to combine the coverage data from all the tox environments run:
 
 # CHANGELOG
 
+## v1.2.1 (2025-07-11)
+
+### Bug fixes
+
+* readme: trigger new version after style changes ([`8b2b5e9`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/8b2b5e93c0f24ae59afaa764abdc508e994946b4))
+
+### Code style
+
+* __init__: imports format ([`6f07790`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/6f07790a04e43736b1c0fbce0eac54d0b661a7cf))
+
+* utils: satisfy flake8 ([`9657474`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/9657474e94a4d9887c4a6b653e0ffa403e666d02))
+
+* readdata: satisfy flake8 ([`36bf6e8`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/36bf6e8be67a2ebd345c5557c2352710bcebed82))
+
+### Continuous integration
+
+* workflow: publish only if the docs are good ([`a663ed3`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/a663ed3d1fd87079a4fd7cf419132a129280a562))
+
+### Testing
+
+* utils: fix imports ([`ddd5369`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/ddd5369b8037f583c6900aea25522a56126c9d32))
+
+## v1.2.0 (2025-07-11)
+
+### Features
+
+* readdata: readSSF() renamed from readSession(), tests added with expected JSON output ([`e2197f6`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/e2197f6bcb032c1bc1a9a7435e024dda763228c4))
+
+* readPDHmeta: routine for reading metadata part from .PDH and .SSF files ([`ea6a1d5`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/ea6a1d554f3763fc05022ae8e4e8909f0993cd43))
+
+### Testing
+
+* readdata: path separator depends on platform ([`1b2866f`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/1b2866f13307c2cf2dedc59f36d7372442ddbfd8))
+
+* readdata: testdata files and testing, using pathlib instead of old os.path ([`aeacfa4`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/aeacfa4a949d7293f2cd3ce5e3004fddf20ecc02))
+
 ## v1.1.0 (2025-07-10)
 
 ### Bug fixes

{jupyter_analysis_tools-1.1.0 → jupyter_analysis_tools-1.2.1}/README.rst

@@ -14,8 +14,8 @@ Yet another Python library with helpers and utilities for data analysis and proc
     :target: https://pypi.org/project/jupyter-analysis-tools
     :alt: PyPI Package latest release
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.1.0.svg
-    :target: https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.1.0...main
+.. |commits-since| image:: https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.2.1.svg
+    :target: https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.2.1...main
     :alt: Commits since latest release
 
 .. |license| image:: https://img.shields.io/pypi/l/jupyter-analysis-tools.svg
@@ -65,9 +65,9 @@ https://BAMresearch.github.io/jupyter-analysis-tools
 Development
 ===========
 
-To run all the tests run::
+Run all tests with::
 
-    tox
+    tox -e py
 
 Note, to combine the coverage data from all the tox environments run:
 

{jupyter_analysis_tools-1.1.0 → jupyter_analysis_tools-1.2.1}/docs/conf.py

@@ -29,7 +29,7 @@ project = "Jupyter Analysis Tools"
 year = "2018-2023"
 author = "Ingo Breßler"
 copyright = "{0}, {1}".format(year, author)
-version = "1.1.0"
+version = "1.2.1"
 release = version
 commit_id = None
 try:

{jupyter_analysis_tools-1.1.0 → jupyter_analysis_tools-1.2.1}/src/jupyter_analysis_tools/__init__.py

@@ -1,12 +1,13 @@
 # -*- coding: utf-8 -*-
 # __init__.py
 
-__version__ = "1.1.0"
+__version__ = "1.2.1"
 
 from .binning import reBin
 from .git import checkRepo, isNBstripoutActivated, isNBstripoutInstalled, isRepo
 from .readdata import readdata
 from .readdata import readdata as readPDH
+from .readdata import readPDHmeta, readSSF
 from .utils import setLocaleUTF8
 from .widgets import PathSelector, showBoolStatus
 

jupyter_analysis_tools-1.2.1/src/jupyter_analysis_tools/readdata.py

@@ -0,0 +1,167 @@
+# -*- coding: utf-8 -*-
+# readdata.py
+
+import warnings
+import xml.etree.ElementTree as et
+from pathlib import Path
+
+import pandas as pd
+
+
+def readdata(fpath, q_range=None, read_csv_args=None, print_filename=True):
+    """Read a datafile pandas Dataframe
+    extract a file_name
+    select q-range: q_min <= q <= q_max
+    """
+    fpath = Path(fpath)
+    if print_filename:
+        print(f"Reading file '{str(fpath)}'")
+    if read_csv_args is None:
+        read_csv_args = dict()
+    if "sep" not in read_csv_args:
+        read_csv_args.update(sep=r"\s+")
+    if "names" not in read_csv_args:
+        read_csv_args.update(names=("q", "I", "e"))
+    if "index_col" not in read_csv_args:
+        read_csv_args.update(index_col=False)
+    # print("f_read_data, read_csv_args:", read_csv_args) # for debugging
+
+    file_ext = fpath.suffix
+    if file_ext.lower() == ".pdh":  # for PDH files
+        nrows = pd.read_csv(
+            fpath,
+            skiprows=2,
+            nrows=1,
+            usecols=[
+                0,
+            ],
+            sep=r"\s+",
+            header=None,
+        ).values[0, 0]
+        read_csv_args.update(skiprows=5, nrows=nrows)
+    df = pd.read_csv(fpath, **read_csv_args)
+
+    # select q-range
+    if q_range is not None:
+        q_min, q_max = q_range
+        df = df[(df.q > q_min) & (df.q < q_max)]
+
+    filename = fpath.stem.split("[")[0]
+    return df, filename
+
+
+def convertValue(val):
+    val = val.strip()
+    try:
+        return int(val)
+    except ValueError:
+        try:
+            return float(val)
+        except ValueError:
+            pass
+    return val
+
+
+def xmlPDHToDict(root):
+    result = {}
+    stack = [(root, result)]
+    while stack:
+        elem, parentCont = stack.pop()
+        elemCont = {}
+        key = elem.attrib.pop("key", None)
+        idx = -1
+        if (
+            not len(list(elem)) and
+            not len(elem.attrib) and
+            not (elem.text and len(elem.text.strip()))
+        ):
+            continue  # skip empty elements with a key only early
+        if elem.tag == "list":
+            elemCont = []
+        else:  # add attributes & values to dict
+            # Attach text, if any
+            if elem.text and len(elem.text.strip()):
+                if elem.tag in ("value", "reference"):
+                    elemCont["value"] = convertValue(elem.text)
+                else:
+                    elemCont["#text"] = convertValue(elem.text)
+            # Attach attributes, if any
+            if elem.attrib:
+                elemCont.update(
+                    {k: convertValue(v) for k, v in elem.attrib.items() if len(v.strip())}
+                )
+            if key == "unit" and "value" in elemCont:  # fix some units
+                elemCont["value"] = elemCont["value"].replace("_", "")
+            if "unit" in elemCont:
+                elemCont["unit"] = elemCont["unit"].replace("_", "")
+            # reduce the extracted dict&attributes
+            idx = elemCont.get("index", -1)  # insert last/append if no index given
+            value = elemCont.get("value", None)
+            if value is not None and (
+                len(elemCont) == 1 or (len(elemCont) == 2 and "index" in elemCont)
+            ):
+                elemCont = value  # contains value only
+        parentKey = elem.tag
+        if key is not None and parentKey in ("list", "value", "group"):
+            # skip one level in hierarchy for these generic containers
+            parentKey = key
+            key = None
+        try:
+            if isinstance(parentCont, list):
+                parentCont.insert(idx, elemCont)
+            elif parentKey not in parentCont:  # add as new list
+                if key is None:  # make a list
+                    parentCont[parentKey] = elemCont
+                else:  # have a key
+                    parentCont[parentKey] = {key: elemCont}
+            else:  # parentKey exists already
+                if (
+                    not isinstance(parentCont[parentKey], list) and
+                    not isinstance(parentCont[parentKey], dict)
+                ):
+                    # if its a plain value before, make a list out of it and append in next step
+                    parentCont[parentKey] = [parentCont[parentKey]]
+                if isinstance(parentCont[parentKey], list):
+                    parentCont[parentKey].append(elemCont)
+                elif key is not None:
+                    parentCont[parentKey].update({key: elemCont})
+                else:  # key is None
+                    parentCont[parentKey].update(elemCont)
+        except AttributeError:
+            raise
+        # reversed for correct order
+        stack += [(child, elemCont) for child in reversed(list(elem))]
+    # fix some entry values, weird Anton Paar PDH format
+    try:
+        oldts = result["fileinfo"]["parameter"]["DateTime"]["value"]
+        # timestamp seems to be based on around 2009-01-01 (a day give or take)
+        delta = ((39 * 365 + 10) * 24 * 3600)
+        # make it compatible to datetime.datetime routines
+        result["fileinfo"]["parameter"]["DateTime"]["value"] = oldts + delta
+    except KeyError:
+        pass
+    return result
+
+
+def readPDHmeta(fp):
+    fp = Path(fp)
+    if fp.suffix.lower() != ".pdh":
+        warnings.warn("readPDHmeta() supports .pdh files only!")
+        return  # for PDH files
+    lines = ""
+    with open(fp) as fd:
+        lines = fd.readlines()
+    nrows = int(lines[2].split()[0])
+    xml = "".join(lines[nrows + 5 :])
+    return xmlPDHToDict(et.fromstring(xml))
+
+
+def readSSF(fp):
+    fp = Path(fp)
+    if fp.suffix.lower() != ".ssf":
+        warnings.warn("readSession() supports .ssf files only!")
+        return  # for PDH files
+    data = ""
+    with open(fp, encoding="utf-8-sig") as fd:
+        data = fd.read()
+    return xmlPDHToDict(et.fromstring(data))

{jupyter_analysis_tools-1.1.0 → jupyter_analysis_tools-1.2.1}/src/jupyter_analysis_tools/utils.py

@@ -89,7 +89,8 @@ def addEnvScriptsToPATH():
     """Prepends the *Scripts* directory of the current Python environment base directory to systems
     PATH variable.
 
-    It is intended for Conda (Miniforge) environments on Windows that do not have this in their PATH environment variable, causing them to miss many commands provided from this location.
+    It is intended for Conda (Miniforge) environments on Windows that do not have this in their PATH
+    environment variable, causing them to miss many commands provided from this location.
     """
     envPath = [p for p in sys.path if p.endswith("Lib")]
     if not envPath:

{jupyter_analysis_tools-1.1.0 → jupyter_analysis_tools-1.2.1}/src/jupyter_analysis_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: jupyter-analysis-tools
-Version: 1.1.0
+Version: 1.2.1
 Summary: Yet another Python library with helpers and utilities for data analysis and processing.
 Author-email: Ingo Breßler <dev@ingobressler.net>
 License: MIT license
@@ -53,8 +53,8 @@ Yet another Python library with helpers and utilities for data analysis and proc
     :target: https://pypi.org/project/jupyter-analysis-tools
     :alt: PyPI Package latest release
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.1.0.svg
-    :target: https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.1.0...main
+.. |commits-since| image:: https://img.shields.io/github/commits-since/BAMresearch/jupyter-analysis-tools/v1.2.1.svg
+    :target: https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.2.1...main
     :alt: Commits since latest release
 
 .. |license| image:: https://img.shields.io/pypi/l/jupyter-analysis-tools.svg
@@ -104,9 +104,9 @@ https://BAMresearch.github.io/jupyter-analysis-tools
 Development
 ===========
 
-To run all the tests run::
+Run all tests with::
 
-    tox
+    tox -e py
 
 Note, to combine the coverage data from all the tox environments run:
 
@@ -127,6 +127,42 @@ Note, to combine the coverage data from all the tox environments run:
 
 # CHANGELOG
 
+## v1.2.1 (2025-07-11)
+
+### Bug fixes
+
+* readme: trigger new version after style changes ([`8b2b5e9`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/8b2b5e93c0f24ae59afaa764abdc508e994946b4))
+
+### Code style
+
+* __init__: imports format ([`6f07790`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/6f07790a04e43736b1c0fbce0eac54d0b661a7cf))
+
+* utils: satisfy flake8 ([`9657474`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/9657474e94a4d9887c4a6b653e0ffa403e666d02))
+
+* readdata: satisfy flake8 ([`36bf6e8`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/36bf6e8be67a2ebd345c5557c2352710bcebed82))
+
+### Continuous integration
+
+* workflow: publish only if the docs are good ([`a663ed3`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/a663ed3d1fd87079a4fd7cf419132a129280a562))
+
+### Testing
+
+* utils: fix imports ([`ddd5369`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/ddd5369b8037f583c6900aea25522a56126c9d32))
+
+## v1.2.0 (2025-07-11)
+
+### Features
+
+* readdata: readSSF() renamed from readSession(), tests added with expected JSON output ([`e2197f6`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/e2197f6bcb032c1bc1a9a7435e024dda763228c4))
+
+* readPDHmeta: routine for reading metadata part from .PDH and .SSF files ([`ea6a1d5`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/ea6a1d554f3763fc05022ae8e4e8909f0993cd43))
+
+### Testing
+
+* readdata: path separator depends on platform ([`1b2866f`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/1b2866f13307c2cf2dedc59f36d7372442ddbfd8))
+
+* readdata: testdata files and testing, using pathlib instead of old os.path ([`aeacfa4`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/aeacfa4a949d7293f2cd3ce5e3004fddf20ecc02))
+
 ## v1.1.0 (2025-07-10)
 
 ### Bug fixes

{jupyter_analysis_tools-1.1.0 → jupyter_analysis_tools-1.2.1}/src/jupyter_analysis_tools.egg-info/SOURCES.txt

@@ -46,5 +46,11 @@ src/jupyter_analysis_tools.egg-info/dependency_links.txt
 src/jupyter_analysis_tools.egg-info/requires.txt
 src/jupyter_analysis_tools.egg-info/top_level.txt
 templates/CHANGELOG.md.j2
+testdata/2015-03-20-Silica.ssf.json
+testdata/2015-03-20-Silica.ssfz
+testdata/S2842 water.json
+testdata/S2842 water.pdh
+testdata/S2843[9].pdh
+tests/readdata.py
 tests/requirements.txt
 tests/utils.py