pynmrstar 3.3.5__cp311-cp311-musllinux_1_2_x86_64.whl → 3.3.6__cp311-cp311-musllinux_1_2_x86_64.whl

pynmrstar/_internal.py

@@ -7,23 +7,19 @@ import zlib
 from datetime import date
 from gzip import GzipFile
 from io import StringIO, BytesIO
+from pathlib import Path
 from typing import Dict, Union, IO, List, Tuple
-from urllib.error import HTTPError, URLError
-from urllib.request import urlopen, Request
+from urllib.error import URLError
+
+import requests
 
 import pynmrstar
 
-__version__: str = "3.3.5"
+__version__: str = "3.3.6"
 min_cnmrstar_version: str = "3.2.0"
 
-# If we have requests, open a session to reuse for the duration of the program run
-try:
-    from requests import session as _requests_session
-    # This replaces the urllib HTTPError if we have requests
-    from requests.exceptions import HTTPError, ConnectionError
-    _session = _requests_session()
-except ModuleNotFoundError:
-    _session = None
+# Create a session to reuse for the duration of the program run
+_session = requests.session()
 
 logger = logging.getLogger('pynmrstar')
 
@@ -81,64 +77,34 @@ def _get_url_reliably(url: str, wait_time: float = 10, raw: bool = False, timeou
 
     global _session
 
-    # If using Requests
-    if _session:
+    try:
+        response = _session.get(url, timeout=timeout,
+                                headers={'Application': f'PyNMRSTAR {__version__}'})
+    except requests.exceptions.ConnectionError:
+        _session = requests.session()
         try:
             response = _session.get(url, timeout=timeout,
                                     headers={'Application': f'PyNMRSTAR {__version__}'})
-        except ConnectionError:
-            _session = _requests_session()
-            try:
-                response = _session.get(url, timeout=timeout,
-                                        headers={'Application': f'PyNMRSTAR {__version__}'})
-            except ConnectionError:
-                raise HTTPError("A ConnectionError was thrown during an attempt to load the entry.")
-
-        # We are rate limited - sleep and try again
-        if response.status_code == 403:
-            if retries > 0:
-                logger.warning(f'We were rate limited. Sleeping for {wait_time} seconds.')
-                time.sleep(wait_time)
-                return _get_url_reliably(url, wait_time=wait_time*2, raw=raw, timeout=timeout,
-                                         retries=retries - 1)
-            else:
-                raise HTTPError("Continued to receive 403 (forbidden, due to rate limit) after multiple wait times.") \
-                    from None
-        if response.status_code == 404:
-            raise KeyError(f"Server returned 404.") from None
-        response.raise_for_status()
-        if raw:
-            return response.content
+        except requests.exceptions.ConnectionError:
+            raise requests.exceptions.HTTPError("A ConnectionError was thrown during an attempt to load the entry.")
+
+    # We are rate limited - sleep and try again
+    if response.status_code == 403:
+        if retries > 0:
+            logger.warning(f'We were rate limited. Sleeping for {wait_time} seconds.')
+            time.sleep(wait_time)
+            return _get_url_reliably(url, wait_time=wait_time * 2, raw=raw, timeout=timeout,
+                                     retries=retries - 1)
         else:
-            return response.text
+            raise requests.exceptions.HTTPError("Continued to receive 403 (forbidden, due to rate limit) after multiple wait times.") \
+                from None
+    if response.status_code == 404:
+        raise KeyError(f"Server returned 404.") from None
+    response.raise_for_status()
+    if raw:
+        return response.content
     else:
-        # Use the built in library
-        try:
-            req = Request(url)
-            req.add_header('Application', f'PyNMRSTAR {__version__}')
-            url_request = urlopen(req, timeout=timeout)
-            serialized_ent = url_request.read()
-            url_request.close()
-
-        except HTTPError as err:
-            if err.code == 404:
-                raise KeyError(f"Server returned 404.") from None
-            # We are rate limited - sleep and try again
-            elif err.code == 403:
-                if retries > 0:
-                    logger.warning(f'We were rate limited. Sleeping for {wait_time} seconds.')
-                    time.sleep(wait_time)
-                    return _get_url_reliably(url, wait_time=wait_time * 2, raw=raw, timeout=timeout,
-                                             retries=retries - 1)
-                else:
-                    raise HTTPError("Continued to receive 403 (forbidden, due to rate limit) after multiple wait "
-                                    "times.") from None
-            else:
-                raise err
-        if raw:
-            return serialized_ent
-        else:
-            return serialized_ent.decode()
+        return response.text
 
 
 def _get_entry_from_database(entry_num: Union[str, int],
@@ -161,7 +127,7 @@ def _get_entry_from_database(entry_num: Union[str, int],
         if "error" in json_data:
             raise RuntimeError('Something wrong with API response.')
         ent = pynmrstar.Entry.from_json(json_data)
-    except (HTTPError, ConnectionError, RuntimeError):
+    except (requests.exceptions.HTTPError, requests.exceptions.ConnectionError, RuntimeError):
         # Can't fall back to FTP for chemcomps
         if entry_num.startswith("chemcomp"):
             raise IOError("Unable to load that chemcomp from the API.")
@@ -176,7 +142,7 @@ def _get_entry_from_database(entry_num: Union[str, int],
             # Use a longer timeout for the timeout
             entry_content = _get_url_reliably(url, raw=False, timeout=20, retries=1)
             ent = pynmrstar.Entry.from_string(entry_content)
-        except HTTPError:
+        except requests.exceptions.HTTPError:
             raise IOError(f"Entry {entry_num} does not exist in the public database.") from None
         except URLError:
             raise IOError("You don't appear to have an active internet connection. Cannot fetch entry.") from None
@@ -206,7 +172,7 @@ def _get_entry_from_database(entry_num: Union[str, int],
     return ent
 
 
-def _interpret_file(the_file: Union[str, IO]) -> StringIO:
+def _interpret_file(the_file: Union[str, Path, IO]) -> StringIO:
     """Helper method returns some sort of object with a read() method.
     the_file could be a URL, a file location, a file object, or a
     gzipped version of any of the above."""
@@ -225,6 +191,9 @@ def _interpret_file(the_file: Union[str, IO]) -> StringIO:
         else:
             with open(the_file, 'rb') as read_file:
                 buffer = BytesIO(read_file.read())
+    elif isinstance(the_file, Path):
+        with open(str(the_file), 'rb') as read_file:
+            buffer = BytesIO(read_file.read())
     else:
         raise ValueError("Cannot figure out how to interpret the file you passed.")
 
@@ -269,7 +238,7 @@ def get_clean_tag_list(item: Union[str, List[str], Tuple[str]]) -> List[Dict[str
 
 
 def write_to_file(nmrstar_object: Union['pynmrstar.Entry', 'pynmrstar.Saveframe'],
-                  file_name: str,
+                  file_name: Union[str, Path],
                   format_: str = "nmrstar",
                   show_comments: bool = True,
                   skip_empty_loops: bool = False,
@@ -287,6 +256,6 @@ def write_to_file(nmrstar_object: Union['pynmrstar.Entry', 'pynmrstar.Saveframe'
     elif format_ == "json":
         data_to_write = nmrstar_object.get_json()
 
-    out_file = open(file_name, "w")
+    out_file = open(str(file_name), "w")
     out_file.write(data_to_write)
     out_file.close()

pynmrstar/_types.py

@@ -0,0 +1,14 @@
+from typing import Dict, Any, List, Union
+
+RowDict          = Dict[str, Any]            # One row: tag → value
+ColumnarDict     = Dict[str, List[Any]]      # One column per tag
+RowMatrix        = List[List[Any]]           # Matrix of rows (format #3)
+FlatRow          = List[Any]                 # One flat row (format #4)
+
+DataInput = Union[
+    RowDict,                 # format #1 – single row
+    List[RowDict],           # format #1 – many rows
+    ColumnarDict,            # format #2 – columnar
+    RowMatrix,               # format #3 – list of lists
+    FlatRow,                 # format #4 – flat list
+]

pynmrstar/entry.py

@@ -3,6 +3,7 @@ import json
 import logging
 import warnings
 from io import StringIO
+from pathlib import Path
 from typing import TextIO, BinaryIO, Union, List, Optional, Dict, Any, Tuple
 
 from pynmrstar import definitions, utils, loop as loop_mod, parser as parser_mod, saveframe as saveframe_mod
@@ -304,13 +305,14 @@ class Entry(object):
 
     @classmethod
     def from_file(cls,
-                  the_file: Union[str, TextIO, BinaryIO],
+                  the_file: Union[str, Path, TextIO, BinaryIO],
                   convert_data_types: bool = False,
                   raise_parse_warnings: bool = False,
                   schema: Schema = None):
         """Create an entry by loading in a file. If the_file starts with
         http://, https://, or ftp:// then we will use those protocols to
-        attempt to open the file.
+        attempt to open the file. the_file can be a string path, pathlib.Path 
+        object, or an open file handle.
         
         Setting convert_data_types to True will automatically convert
         the data loaded from the file into the corresponding python type as
@@ -956,7 +958,7 @@ class Entry(object):
 
         return errors
 
-    def write_to_file(self, file_name: str, format_: str = "nmrstar", show_comments: bool = True,
+    def write_to_file(self, file_name: Union[str, Path], format_: str = "nmrstar", show_comments: bool = True,
                       skip_empty_loops: bool = False, skip_empty_tags: bool = False) -> None:
         """ Writes the entry to the specified file in NMR-STAR format.
 

pynmrstar/loop.py

@@ -4,10 +4,12 @@ from copy import deepcopy
 from csv import reader as csv_reader, writer as csv_writer
 from io import StringIO
 from itertools import chain
+from pathlib import Path
 from typing import TextIO, BinaryIO, Union, List, Optional, Any, Dict, Callable, Tuple
 
 from pynmrstar import definitions, utils, entry as entry_mod
 from pynmrstar._internal import _json_serialize, _interpret_file
+from pynmrstar._types import DataInput
 from pynmrstar.exceptions import InvalidStateError
 from pynmrstar.parser import Parser
 from pynmrstar.schema import Schema
@@ -294,7 +296,7 @@ class Loop(object):
 
     @classmethod
     def from_file(cls,
-                  the_file: Union[str, TextIO, BinaryIO],
+                  the_file: Union[str, Path, TextIO, BinaryIO],
                   csv: bool = False,
                   convert_data_types: bool = False,
                   raise_parse_warnings: bool = False,
@@ -302,7 +304,8 @@ class Loop(object):
         """Create a loop by loading in a file. Specify csv=True if
         the file is a CSV file. If the_file starts with http://,
         https://, or ftp:// then we will use those protocols to attempt
-        to open the file.
+        to open the file. the_file can be a string path, pathlib.Path object,
+        or an open file handle.
 
         Setting convert_data_types to True will automatically convert
         the data loaded from the file into the corresponding python type as
@@ -458,49 +461,66 @@ class Loop(object):
 
         return True
 
-    def add_data(self,
-                 data: Union[List[dict], Dict[str, List], List[Union[str, float, int]], List[List[Any]]],
-                 rearrange: bool = False,
-                 convert_data_types: bool = False,
-                 schema: Schema = None):
-        """Add data to a loop. You can provide the data to add organized in four different ways, though the first
-        two are recommended for new code. The other two (#3 and #4) are preserved for sake of existing code (written
-        prior to version 3.3) and for niche use cases:
-
-        1: You can provide a list of dictionaries of tags to add. For example,
-        ``[{'name': 'Jeff', 'location': 'Connecticut'}, {'name': 'Chad', 'location': 'Madison'}]`` will add two new
-        rows, and set the values of the tags ``name`` and ``location`` to the values provided. If there are other
-        tags in the loop, they will be assigned null values for the rows corresponding to the tags added.
-
-        2: You can provide a dictionary of lists, as such (corresponds to adding the same ultimate data as in the
-        example #1): ``{'name': ['Jeff', 'Chad'], 'location': ['Connecticut', 'Madison']}``. This will also create
-        two new rows in the loop and assign the values provided.
-        
-        3: You can provide a list of lists of tag values to add. In this case, each list must have the same tag
-        values (and order of tags) as the known tags present in the loop. To correspond to the above examples, the data
-        would look like: ``[['Jeff', 'Connecticut'], ['Chad', 'Madison']]``. Adding data this way requires both that
-        you provide values for all tags present in the loop, and that you provide the values in the same order that the
-        tags already are already defined in the loop.
-
-        4. You can provide a single list of tag values to add. In the most simple case, that would correspond to just
-        adding one row of data in the same was as in #3 above, as such: ``['Jeff', 'Connecticut']``. In a more
-        complicated example, you could also add data (corresponding to example #1 and #2) as such:
-        ``['Jeff', 'Connecticut', 'Chad', 'Madison']`` - but if you provide data this way, you must set
-         ``rearrange=True``. This usage is strongly discouraged, but exists for legacy reasons.
-
-        :param data: See the docstring for the method.
-        :type data: Union[List[dict], Dict[str, List], List[Union[str, float, int]], List[List[Any]]]
-        :param convert_data_types: If true, converts data you provide into the data type defined in the dictionary.
-            For example, if you provided the string '5' for the tag ``_Atom_chem_shift.Val``, it would automatically
-            be converted to a float while being added. This is mainly useful for parsers, as your data is probably
-            already in a format that is usable for you.
-        :type convert_data_types: bool
-        :param rearrange: If true, rearrange data provided in method #4 as necessary to fit in the loop. This only
-            exists for parsers, and it's use is strongly discouraged.
-        :type rearrange: bool
-        :param schema: A pynmrstar Schema object, which will be used to determine data types if convert_data_types
-            is True.
-        :type schema: pynmrstar.Schema
+    def add_data(
+            self,
+            data: DataInput,
+            rearrange: bool = False,
+            convert_data_types: bool = False,
+            schema: Union[Schema, None] = None,
+    ) -> None:
+        """
+        Add data to a loop.
+
+        You can supply *data* in **four** canonical formats.  Formats #1 and #2
+        are the most convenient; the others are retained mainly for legacy code.
+
+        1. **Row‑oriented dictionaries**  *(preferred)*
+           • a **list** of dictionaries,
+           where each dictionary represents one row::
+
+               [{'name': 'Jeff', 'location': 'Connecticut'},
+                {'name': 'Chad', 'location': 'Madison'}]
+
+        2. **Column‑oriented dictionary of lists**
+           A dictionary mapping each tag to a list of values (or to a single
+           scalar)::
+
+               {'name': ['Jeff', 'Chad'],
+                'location': ['Connecticut', 'Madison']}
+
+           All value‑lists must be the same length; that length determines the
+           number of rows created.
+
+        3. **Matrix of values**
+           A list of lists whose inner order exactly matches the loop’s current
+           tag order::
+
+               [['Jeff', 'Connecticut'],
+                ['Chad', 'Madison']]
+
+        4. **Flat list of values**
+           A single list whose length is either:
+           • exactly the number of tags (adds one row), or
+           • any multiple of that length **when** ``rearrange=True``::
+
+               ['Jeff', 'Connecticut']                          # one row
+               ['Jeff', 'Connecticut', 'Chad', 'Madison']       # two rows (requires rearrange=True)
+
+           This form is discouraged and kept only for backward compatibility.
+
+        Parameters
+        ----------
+        data
+            The data to add, in any of the formats described above.
+        rearrange
+            Only used with format #4.  When ``True`` the flat list is split into
+            evenly sized rows.  Rarely needed outside of old parsers.
+        convert_data_types
+            If ``True`` each value is converted to the type defined in *schema*
+            before insertion.
+        schema
+            A :class:`pynmrstar.Schema` instance used when
+            ``convert_data_types`` is ``True``.
         """
 
         if not data:
@@ -564,7 +584,8 @@ class Loop(object):
                 # Add the user data
                 pending_data.append(data)
         else:
-            raise ValueError("Your data did not match one of the supported types.")
+            raise ValueError("Your data did not match one of the supported types. Please review the documentation for "
+                             "proper usage of this function.")
 
         # Auto convert data types if option set
         if convert_data_types:

pynmrstar/saveframe.py

@@ -2,6 +2,7 @@ import json
 import warnings
 from csv import reader as csv_reader, writer as csv_writer
 from io import StringIO
+from pathlib import Path
 from typing import TextIO, BinaryIO, Union, List, Optional, Any, Dict, Iterable, Tuple
 
 from pynmrstar import definitions, entry as entry_mod, loop as loop_mod, parser as parser_mod, utils
@@ -346,7 +347,7 @@ class Saveframe(object):
 
     @classmethod
     def from_file(cls,
-                  the_file: Union[str, TextIO, BinaryIO],
+                  the_file: Union[str, Path, TextIO, BinaryIO],
                   csv: bool = False,
                   convert_data_types: bool = False,
                   raise_parse_warnings: bool = False,
@@ -354,7 +355,8 @@ class Saveframe(object):
         """Create a saveframe by loading in a file. Specify csv=True is
         the file is a CSV file. If the_file starts with http://,
         https://, or ftp:// then we will use those protocols to attempt
-        to open the file.
+        to open the file. the_file can be a string path, pathlib.Path object,
+        or an open file handle.
 
         Setting convert_data_types to True will automatically convert
         the data loaded from the file into the corresponding python type as
@@ -998,7 +1000,7 @@ class Saveframe(object):
         return errors
 
     def write_to_file(self,
-                      file_name: str,
+                      file_name: Union[str, Path],
                       format_: str = "nmrstar",
                       show_comments: bool = True,
                       skip_empty_loops: bool = False,

{pynmrstar-3.3.5.dist-info → pynmrstar-3.3.6.dist-info}/METADATA

@@ -1,11 +1,12 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pynmrstar
-Version: 3.3.5
+Version: 3.3.6
 Summary: PyNMR-STAR provides tools for reading, writing, modifying, and interacting with NMR-STAR files. Maintained by the BMRB.
 Home-page: https://github.com/uwbmrb/PyNMRSTAR
 Author: Jon Wedell
-Author-email: wedell@uchc.edu
+Author-email: Jon Wedell <wedell@uchc.edu>
 License: MIT
+Project-URL: Homepage, https://github.com/bmrb-io/PyNMRSTAR
 Keywords: bmrb,parser,nmr,nmrstar,biomagresbank,biological magnetic resonance bank
 Classifier: Development Status :: 6 - Mature
 Classifier: Environment :: Console
@@ -29,6 +30,10 @@ Requires-Python: >=3.7
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: requests<=3,>=2.21.0
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
 
 Welcome to PyNMR-STAR!
 ======================================

pynmrstar-3.3.6.dist-info/RECORD

@@ -0,0 +1,20 @@
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+pynmrstar/__init__.py,sha256=z9uQkhmqipDrLHpEk81w7y7HEgepEcKyK7ZWr8YavJA,1967
+pynmrstar/_internal.py,sha256=sf_qxTXdWejDLn2fqEqKr-wC0OtNHNgDud3AurGj3OA,10756
+pynmrstar/_types.py,sha256=INDwmnS3s1RkLg64A--hoJyZNnWJl6cHP5HTRXaO9EY,626
+pynmrstar/definitions.py,sha256=H4X8POb0CsA9lv8tiLupH0wBzKPdyy5OZCe0A1OqZiU,1510
+pynmrstar/entry.py,sha256=NtEyXt4MUFEZ0REnGyeOhTMKEwqot3XmWE8_ENwciC8,46369
+pynmrstar/exceptions.py,sha256=xJlGbHB_QXMiNWuU_6livAQBMljBuCba50WA_K9pIbc,1449
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+pynmrstar-3.3.6.dist-info/RECORD,,
+pynmrstar-3.3.6.dist-info/licenses/LICENSE,sha256=pAZXnNE2dxxwXFIduGyn1gpvPefJtUYOYZOi3yeGG94,1068

{pynmrstar-3.3.5.dist-info → pynmrstar-3.3.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.5.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: false
 Tag: cp311-cp311-musllinux_1_2_x86_64
 

pynmrstar-3.3.5.dist-info/RECORD

@@ -1,19 +0,0 @@
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-pynmrstar/loop.py,sha256=46vAeXMtKaSovLzFhhiFQCz1nsNqOJPSVpkTTa9tbtg,51892
-pynmrstar/exceptions.py,sha256=xJlGbHB_QXMiNWuU_6livAQBMljBuCba50WA_K9pIbc,1449
-pynmrstar/schema.py,sha256=tJsVHkVQR8glvchFBzlRvGDpx2HxS76eucAjR_aKVog,15779
-pynmrstar/_internal.py,sha256=GNWZPAKI7swRfqndVKamFyATNdNa_3nhocTvzT-fM4Y,12068
-pynmrstar/parser.py,sha256=cYnRBkQAdXJU_HY6WCcWMY0Rq2weDyr1hxiWOoQbNfg,15546
-pynmrstar/definitions.py,sha256=H4X8POb0CsA9lv8tiLupH0wBzKPdyy5OZCe0A1OqZiU,1510
-pynmrstar/__init__.py,sha256=z9uQkhmqipDrLHpEk81w7y7HEgepEcKyK7ZWr8YavJA,1967
-pynmrstar/utils.py,sha256=rd7JkVM9B7gMiveO0RhH6YtoJTB0CUiggsPtSVzmvl8,4662
-pynmrstar/entry.py,sha256=BcwVtSdfcDj4NWzmWvSbwilG9whxTk6CyZUbR15mLBk,46240
-pynmrstar/saveframe.py,sha256=5p-_NWi2nEju2FtJG5zm1aSdJrSZi_5lkCMIpTHWXYI,44133
-pynmrstar/reference_files/comments.str,sha256=vOGWBs5XU3ddNyROkVOhaPwGb8kx5stoChgo6ICBMio,9942
-pynmrstar/reference_files/schema.csv,sha256=BfAJyjfDQaZakdEL5V97dTSDxwgxQZCIp1DeKEhT65w,3694703
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