imas-python 0.1.dev1628__py3-none-any.whl → 0.1.dev1630__py3-none-any.whl

imas/__init__.py

@@ -25,10 +25,7 @@ from . import (
     util,
 )
 
-PUBLISHED_DOCUMENTATION_ROOT = (
-    "https://sharepoint.iter.org/departments/POP/CM/IMDesign/"
-    "Code%20Documentation/imas-python-doc"
-)
+PUBLISHED_DOCUMENTATION_ROOT = "https://imas-python.readthedocs.io/en/latest/"
 """URL to the published documentation."""
 OLDEST_SUPPORTED_VERSION = _V("3.22.0")
 """Oldest Data Dictionary version that is supported by imas-python."""

imas/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.dev1628'
-__version_tuple__ = version_tuple = (0, 1, 'dev1628')
+__version__ = version = '0.1.dev1630'
+__version_tuple__ = version_tuple = (0, 1, 'dev1630')

imas/dd_helpers.py

@@ -4,35 +4,30 @@
 
 import logging
 import os
-import re
 import shutil
-import subprocess
-from io import BytesIO
 from pathlib import Path
-from typing import Sequence, Tuple, Union
-from urllib.request import urlopen
+from typing import Tuple
 from zipfile import ZIP_DEFLATED, ZipFile
 
 from packaging.version import Version as V
+from saxonche import PySaxonProcessor
 
 logger = logging.getLogger(__name__)
 
 _idsdef_zip_relpath = Path("imas/assets/IDSDef.zip")
 _build_dir = Path("build")
-_saxon_local_default_name = "saxon9he.jar"  # For pre-3.30.0 builds
-_saxon_regex = "saxon((.(?!test|xqj))*).jar"  # Can be used in re.match
 
 
 def prepare_data_dictionaries():
     """Build IMAS IDSDef.xml files for each tagged version in the DD repository
-    1. Search for saxon or download it
+    1. Use saxonche for transformations
     2. Clone the DD repository (ask for user/pass unless ssh key access is available)
     3. Generate IDSDef.xml and rename to IDSDef_${version}.xml
     4. Zip all these IDSDefs together and include in wheel
     """
+    print("prepare_data_dictionaries")
     from git import Repo
 
-    saxon_jar_path = get_saxon()
     repo: Repo = get_data_dictionary_repo()
     if repo:
         newest_version_and_tag = (V("0"), None)
@@ -41,7 +36,7 @@ def prepare_data_dictionaries():
             if V(str(tag)) > V("3.21.1"):
                 newest_version_and_tag = max(newest_version_and_tag, version_and_tag)
                 logger.debug("Building data dictionary version %s", tag)
-                build_data_dictionary(repo, tag, saxon_jar_path)
+                build_data_dictionary(repo, tag)
 
         logger.info("Creating zip file of DD versions")
 
@@ -68,105 +63,6 @@ def prepare_data_dictionaries():
                 dd_zip.write(filename, arcname=arcname)
 
 
-# pre 3.30.0 versions of the DD have the `saxon9he.jar` file path hardcoded
-# in their makefiles. To be sure we can build everything, we link whatever
-# saxon we can find to a local file called saxon9he.jar
-def get_saxon() -> Path:
-    """Search for saxon*.jar and return the path or download it.
-    The DD build works by having Saxon in the CLASSPATH, called saxon9he.jar
-    until DD version 3.30.0. After 3.30.0 Saxon is found by the SAXONJARFILE env
-    variable. We will 'cheat' a little bit later by symlinking saxon9he.jar to
-    any version of saxon we found.
-
-    Check:
-    1. CLASSPATH
-    2. `which saxon`
-    3. /usr/share/java/*
-    4. or download it
-    """
-
-    local_saxon_path = Path.cwd() / _saxon_local_default_name
-    if local_saxon_path.exists():
-        logger.debug("Something already at '%s' not creating anew", local_saxon_path)
-        return local_saxon_path
-
-    saxon_jar_origin = Path(
-        find_saxon_classpath()
-        or find_saxon_bin()
-        or find_saxon_jar()
-        or download_saxon()
-    )
-    logger.info("Found Saxon JAR '%s'", saxon_jar_origin)
-    if saxon_jar_origin.name != _saxon_local_default_name:
-        try:
-            os.symlink(saxon_jar_origin, local_saxon_path)
-        except FileExistsError:
-            # Another process could have created the symlink while we were searching
-            logger.debug(
-                "Link '%s' exists, parallel process might've created it",
-                local_saxon_path,
-            )
-        return local_saxon_path
-    return saxon_jar_origin
-
-
-def find_saxon_jar():
-    # This finds multiple versions on my system, but they are symlinked together.
-    # take the shortest one.
-    jars = [
-        path
-        for path in Path("/usr/share/java").rglob("*")
-        if re.match(_saxon_regex, path.name, flags=re.IGNORECASE)
-    ]
-
-    if jars:
-        saxon_jar_path = min(jars, key=lambda x: len(x.parts))
-        return saxon_jar_path
-
-
-def find_saxon_classpath():
-    """Search JAVAs CLASSPATH for a Saxon .jar"""
-    classpath = os.environ.get("CLASSPATH", "")
-    for part in re.split(";|:", classpath):
-        if (
-            part.endswith(".jar")
-            and part.split("/")[-1].startswith("saxon")
-            and "test" not in part
-            and "xqj" not in part
-        ):
-            return part
-
-
-def find_saxon_bin():
-    """Search for a saxon executable"""
-    saxon_bin = shutil.which("saxon")
-    if saxon_bin:
-        with open(saxon_bin, "r") as file:
-            for line in file:
-                saxon_jar_path = re.search("[^ ]*saxon[^ ]*jar", line)
-                if saxon_jar_path:
-                    return saxon_jar_path.group(0)
-
-
-def download_saxon():
-    """Downloads a zipfile containing Saxon and extract it to the current dir.
-    Return the full path to Saxon. This can be any Saxon version. Scripts that
-    wrap this should probably manipulate either the name of this file, and/or
-    the CLASSPATH"""
-
-    SAXON_PATH = "https://github.com/Saxonica/Saxon-HE/releases/download/SaxonHE10-9/SaxonHE10-9J.zip"  # noqa: E501
-
-    resp = urlopen(SAXON_PATH, timeout=120.0)
-    zipfile = ZipFile(BytesIO(resp.read()))
-    # Zipfile has a list of the ZipInfos. Look inside for a Saxon jar
-    for file in zipfile.filelist:
-        if re.match(_saxon_regex, file.filename, flags=re.IGNORECASE):
-            path = zipfile.extract(file)
-            del zipfile
-            return path
-    raise FileNotFoundError(f"No Saxon jar found in given zipfile '{SAXON_PATH}'")
-
-
 def get_data_dictionary_repo() -> Tuple[bool, bool]:
     try:
         import git  # Import git here, the user might not have it!
@@ -216,47 +112,33 @@ def get_data_dictionary_repo() -> Tuple[bool, bool]:
     return repo
 
 
-def _run_data_dictionary(
-    args: Union[Sequence, str], tag: str, saxon_jar_path: str
-) -> int:
-    """Run in a Data Dictionary environment. Used e.g. to run the DD Makefile
+def _run_xsl_transformation(
+    xsd_file: Path, xsl_file: Path, tag: str, output_file: Path
+) -> None:
+    """
+    This function performs an XSL transformation using Saxon-HE (saxonche)
+    with the provided XSD file,  XSL file, tag, and output file.
 
     Args:
-        args: The "args" argument directly passed to :func:`subprocess.run`,
-            e.g. ``["make", "clean"]``
-        tag: The DD version tag that will be printed on error
-        saxon_jar_path: The path to the saxon jar; Added to CLASSPATH and used
-            to generate the DD
+        xsd_file (Path): XML Schema Definition (XSD) file
+        xsl_file (Path): The `xsl_file` parameter
+        tag (str): tag name to provide to 'DD_GIT_DESCRIBE' parameter
+        output_file (Path): The `output_file` parameter for resulting xml
     """
-    env = os.environ.copy()
-    env["CLASSPATH"] = f"{saxon_jar_path}:{env.get('CLASSPATH', '')}"
-    result = subprocess.run(
-        args,
-        bufsize=0,
-        capture_output=True,
-        cwd=os.getcwd() + "/data-dictionary",
-        env=env,
-        text=True,
-    )
-
-    if result.returncode != 0:
-        logger.warning("Error making DD version %s, make reported:", tag)
-        logger.warning("CLASSPATH ='%s'", saxon_jar_path)
-        logger.warning("PATH = '%s'", os.environ.get("PATH", ""))
-        logger.warning("stdout = '%s'", result.stdout.strip())
-        logger.warning("stderr = '%s'", result.stderr.strip())
-        logger.warning("continuing without DD version %s", tag)
-    else:
-        logger.debug(
-            "Successful make for DD %s.\n-- Make stdout --\n%s\n-- Make stderr --\n%s",
-            tag,
-            result.stdout,
-            result.stderr,
+    with PySaxonProcessor(license=False) as proc:
+        logger.debug("Initializing Saxon Processor")
+        xsltproc = proc.new_xslt30_processor()
+        xdm_ddgit = proc.make_string_value(tag)
+        xsltproc.set_parameter("DD_GIT_DESCRIBE", xdm_ddgit)
+        xsltproc.transform_to_file(
+            source_file=str(xsd_file),
+            stylesheet_file=str(xsl_file),
+            output_file=str(output_file),
         )
-    return result.returncode
+        logger.info("Transformation complete: %s -> %s", xsd_file, output_file)
 
 
-def build_data_dictionary(repo, tag: str, saxon_jar_path: str, rebuild=False) -> None:
+def build_data_dictionary(repo, tag: str, rebuild=False) -> None:
     """Build a single version of the data dictionary given by the tag argument
     if the IDS does not already exist.
 
@@ -266,8 +148,6 @@ def build_data_dictionary(repo, tag: str, saxon_jar_path: str, rebuild=False) ->
     Args:
         repo: Repository object containing the DD source code
         tag: The DD version tag that will be build
-        saxon_jar_path: The path to the saxon jar; Added to CLASSPATH and used
-            to generate the DD
         rebuild: If true, overwrites existing pre-build tagged DD version
     """
     _build_dir.mkdir(exist_ok=True)
@@ -278,22 +158,11 @@ def build_data_dictionary(repo, tag: str, saxon_jar_path: str, rebuild=False) ->
         return
 
     repo.git.checkout(tag, force=True)
-    if _run_data_dictionary(["make", "clean"], tag, saxon_jar_path) != 0:
-        return
-    if _run_data_dictionary(["make", "IDSDef.xml"], tag, saxon_jar_path) != 0:
-        return
 
-    # copy and delete original instead of move (to follow symlink)
-    IDSDef = Path("data-dictionary/IDSDef.xml")
-    try:
-        shutil.copy(
-            IDSDef,  # Hardcoded in access-layer makefile
-            result_xml,
-            follow_symlinks=True,
-        )
-    except shutil.SameFileError:
-        pass
-    IDSDef.unlink(missing_ok=True)
+    # Perform the XSL transformation with saxonche
+    dd_xsd = Path("data-dictionary/dd_data_dictionary.xml.xsd")
+    dd_xsl = Path("data-dictionary/dd_data_dictionary.xml.xsl")
+    _run_xsl_transformation(dd_xsd, dd_xsl, tag.name, result_xml)
 
 
 if __name__ == "__main__":

imas/ids_structure.py

@@ -252,8 +252,8 @@ class IDSStructure(IDSBase):
                 "Iterating over non-empty nodes of a lazy loaded IDS will skip nodes "
                 "that are not loaded. Set accept_lazy=True to continue. "
                 "See the documentation for more information: "
-                "https://sharepoint.iter.org/departments/POP/CM/IMDesign/"
-                "Code%20Documentation/imas-python-doc/generated/imas.ids_structure."
+                "https://imas-python.readthedocs.io/en/latest"
+                "/generated/imas.ids_structure."
                 "IDSStructure.html#imas.ids_structure.IDSStructure.iter_nonempty_"
             )
         for child in self._children:

{imas_python-0.1.dev1628.dist-info → imas_python-0.1.dev1630.dist-info}/METADATA

@@ -1,8 +1,8 @@
 Metadata-Version: 2.2
 Name: imas-python
-Version: 0.1.dev1628
+Version: 0.1.dev1630
 Summary: Pythonic wrappers for the IMAS Access Layer
-Author: imas-python Developers
+Author: imas-python developers
 Author-email: Olivier Hoenen <olivier.hoenen@iter.org>
 License:                   GNU LESSER GENERAL PUBLIC LICENSE
                                Version 3, 29 June 2007
@@ -212,6 +212,8 @@ Requires-Dist: click
 Requires-Dist: importlib_resources; python_version < "3.9"
 Requires-Dist: packaging
 Requires-Dist: xxhash>=2
+Requires-Dist: saxonche
+Requires-Dist: gitpython
 Provides-Extra: all
 Requires-Dist: imas[docs,h5py,imas-core,netcdf,test]; extra == "all"
 Provides-Extra: docs
@@ -247,7 +249,7 @@ Data Model.
 Install steps are described in the documentation generated from `/docs/source/installing.rst`.
 
 Documentation is autogenerated from the source using [Sphinx](http://sphinx-doc.org/)
-and can be found at the [ITER sharepoint](https://sharepoint.iter.org/departments/POP/CM/IMDesign/Code%20Documentation/IMAS-doc/index.html)
+and can be found at the [readthedocs](https://imas-python.readthedocs.io/en/latest/)
 
 The documentation can be manually generated by installing sphinx and running:
 

{imas_python-0.1.dev1628.dist-info → imas_python-0.1.dev1630.dist-info}/RECORD

@@ -1,9 +1,9 @@
-imas/__init__.py,sha256=TcIsTA05yiteecXpGnhm0fKw_cEHIc4TJUHC1iP5fJo,940
+imas/__init__.py,sha256=9OHpTf8gCl7BJVU7U2bf9kWatBNNAhFZdgoFPcHeNQU,878
 imas/__main__.py,sha256=2qXoC0HzV4xkPQAvdubHC4rnK3G6f_2PT9TkkCHYXk8,418
 imas/_util.py,sha256=FXX13glhmgSiw-0LtjH0xv3YlM3Pa9X4jl9yz9Uv7Vs,9484
-imas/_version.py,sha256=37tfNBIVZOWgN0uOLXfG18OnUZiyzRJUR_f3wVBwCA8,425
+imas/_version.py,sha256=OpP0F45Ue1X9KS-OpxRWnRU3SYVrRth3FtH_kqSiU4Q,425
 imas/db_entry.py,sha256=O76bfCfmH3jlZE8eJmnmPiDNqZYpwo3ooQeHOL83mE4,31767
-imas/dd_helpers.py,sha256=c1uvR7TvFvOLGUhj1h0PtPMm69CGBjtWrv2AC8FvU2I,10844
+imas/dd_helpers.py,sha256=tKPbnje62PGNGTclpC_VKg9b-mZWy9VvkICqwzkdiGA,6314
 imas/dd_zip.py,sha256=Sz2xP-oWyhmmqEN-JGGNizieGZH8CJ6JlCjqN_0fMvw,10330
 imas/exception.py,sha256=iqsxl6M1gEjJO8YP9UBYt5OQk7faGx0EIs1XJ4YJ71U,3750
 imas/ids_base.py,sha256=zDckve7poXO9vbKPsi_17FjKMTKd6QADork7H7wIS7o,5439
@@ -17,12 +17,12 @@ imas/ids_metadata.py,sha256=kpyNKXB9-aQpjdj1df10qKZIJ7-HC5BuDOhGyhX9YMI,12258
 imas/ids_path.py,sha256=rqucboH8wO4-njy8d6lUffnfHA6L2b81wh8AJ6Y_gbU,10446
 imas/ids_primitive.py,sha256=3s0y0nxPSXjAoXEYUvsmevWOqmfCBnct-ySr_f2oU9k,16810
 imas/ids_struct_array.py,sha256=BFBa1wSZFAlZguExCTA56D8RfnaLv-nbxDIz9fMhcGE,8292
-imas/ids_structure.py,sha256=IqfPxjAJtDE0aM0sdyEfbvHiD3yIenX7eMsoACi--L4,13155
+imas/ids_structure.py,sha256=0DRudIturYE2Aw_Jb22zBZCd_zyA0-lg8YOEI7Y_iso,13107
 imas/ids_toplevel.py,sha256=YHWZewK8JYf34pYzF_oooMILZAHgnuWCFtr0_JFjmzI,14915
 imas/setup_logging.py,sha256=auFmrFHh1CA6LVQVwo6WWebUIbCpA_7UedQ6G4h5JzM,1874
 imas/training.py,sha256=JGYjpCubUJDb_Rg0QaaDhNkBHc4Qc376U9fRq24NVXc,1576
 imas/util.py,sha256=dG282-l7m2U_VhjZ0VnQ-BpsWrzgKSxUZ1AZf-_wDOY,17822
-imas/assets/IDSDef.zip,sha256=iThF2_DSZXg18tv1elvtA9Maa4toX6vyytrm5bLaleE,27383258
+imas/assets/IDSDef.zip,sha256=P--G2iMe4FYakrJC9PS_Hsc4JR8CK8S9zsdwKuWF_ZI,27383258
 imas/assets/IDSDef2MDSpreTree.xsl,sha256=V9eDmDnxe6oYhDP81gmdYip8cF2yST9dGxmZBaATLdA,7296
 imas/assets/IDS_fake_toplevel.xml,sha256=TJhukQuDHHVTW2U7fK_-KmTQiYOFZMY-ECZXBHQE2mk,18683
 imas/assets/IDS_minimal.xml,sha256=5B6c0J-WPzSChHWwpLPRkNawx9m6v8BM5nC0OQFnWcQ,1740
@@ -101,9 +101,9 @@ imas/test/test_str_1d.py,sha256=d6GrmV4OYG9f4ludjZBmuqyKOM9XIExTqMh8aQ1UJcQ,3453
 imas/test/test_time_slicing.py,sha256=FwbdggRJ75Suc268-89daCSaVXhzl8pZZm3Od13EiR4,6959
 imas/test/test_uda_support.py,sha256=AmakuexebZfJ2-vk_DHfNRPwHmNM2RnwzXqT0eWwWJ0,338
 imas/test/test_util.py,sha256=BW5EbL-QDIrJNH7tjBgqOacJY0TXvMidXVKpIVZlv1I,6775
-imas_python-0.1.dev1628.dist-info/LICENSE.txt,sha256=RzxtV7MG0zbF6dDvQsaZ1OKsHZ7CRyeILenjUIol5rs,7651
-imas_python-0.1.dev1628.dist-info/METADATA,sha256=o0xC-_YVQcYLN0m7_BgfyqUbtV_wbApliHE-c3Ftt9Q,13452
-imas_python-0.1.dev1628.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-imas_python-0.1.dev1628.dist-info/entry_points.txt,sha256=e8oXj2SLwyFEiBeJRaAXRc9EYQ8eHWWn7NWdjixjeDM,99
-imas_python-0.1.dev1628.dist-info/top_level.txt,sha256=_WFOlA1rmpYm0T73sNo5Ntvs7S3x4cR7UE8Oy5I5eJA,5
-imas_python-0.1.dev1628.dist-info/RECORD,,
+imas_python-0.1.dev1630.dist-info/LICENSE.txt,sha256=RzxtV7MG0zbF6dDvQsaZ1OKsHZ7CRyeILenjUIol5rs,7651
+imas_python-0.1.dev1630.dist-info/METADATA,sha256=lR2NVbzINbR2-FqVrbHjeDerYMDVCS9oayI-4Dg9jAM,13446
+imas_python-0.1.dev1630.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+imas_python-0.1.dev1630.dist-info/entry_points.txt,sha256=e8oXj2SLwyFEiBeJRaAXRc9EYQ8eHWWn7NWdjixjeDM,99
+imas_python-0.1.dev1630.dist-info/top_level.txt,sha256=_WFOlA1rmpYm0T73sNo5Ntvs7S3x4cR7UE8Oy5I5eJA,5
+imas_python-0.1.dev1630.dist-info/RECORD,,