cellpy 1.0.1.post3__tar.gz → 1.0.2__tar.gz

{cellpy-1.0.1.post3 → cellpy-1.0.2}/HISTORY.md

@@ -1,5 +1,18 @@
 # History
 
+## 1.0.2
+
+* Batch: `only_selected` keyword added for concatenating summaries choosing only selected cells in the pages (selected==1)
+* General: Add option to specify custom_log_path and path to logging config json in get() (#326) by @morrowrasmus
+* Batch: implement wide format for collectors to csv
+* Batch: adding more columns to pages (model, selected, nom_cap_specifics)
+* General: Implemented lazy import to speed up loading of cellpy
+* General: Added _absolute cols in the summary
+* General: Add basic support for reading parquet for custom instruments (#322) by @morrowrasmus
+* Utils: General improvements in plotutils
+* General: Dropped support for python 3.9 and added support for python 3.12 (and probably beyond) by upgrading `OtherPaths`
+* Bug fixes.
+
 ## 1.0.1
 
 * Utils: `example_data` now includes auto-download of example data

{cellpy-1.0.1.post3 → cellpy-1.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: cellpy
-Version: 1.0.1.post3
+Version: 1.0.2
 Summary: Extract and manipulate data from battery data testers.
 Home-page: https://github.com/jepegit/cellpy
 Author: Jan Petter Maehlen
@@ -13,6 +13,7 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 License-File: AUTHORS.md
@@ -40,6 +41,7 @@ Requires-Dist: jinja2_time
 Requires-Dist: tables
 Requires-Dist: ipykernel
 Requires-Dist: rich
+Requires-Dist: charset-normalizer
 Provides-Extra: batch
 Requires-Dist: ipython; extra == "batch"
 Requires-Dist: jupyter; extra == "batch"
@@ -55,6 +57,18 @@ Requires-Dist: plotly; extra == "all"
 Requires-Dist: seaborn; extra == "all"
 Requires-Dist: kaleido==0.1.*; extra == "all"
 Requires-Dist: lmfit; extra == "all"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
 
 <img src="https://raw.githubusercontent.com/jepegit/cellpy/master/docs/_static/cellpy-icon-long.svg" height="100" alt="cellpy-icon">
 
@@ -67,7 +81,7 @@ Requires-Dist: lmfit; extra == "all"
 
 This Python Package was developed to help the
 researchers at IFE, Norway, in their cumbersome task of
-interpreting and handling data from cycling tests of
+interpreting and handling data from cycling tests of batteries and cells.
 
 ## Features
 
@@ -122,6 +136,19 @@ please have a look at [Contributing Guidelines](CONTRIBUTING.md).
 
 # History
 
+## 1.0.2
+
+* Batch: `only_selected` keyword added for concatenating summaries choosing only selected cells in the pages (selected==1)
+* General: Add option to specify custom_log_path and path to logging config json in get() (#326) by @morrowrasmus
+* Batch: implement wide format for collectors to csv
+* Batch: adding more columns to pages (model, selected, nom_cap_specifics)
+* General: Implemented lazy import to speed up loading of cellpy
+* General: Added _absolute cols in the summary
+* General: Add basic support for reading parquet for custom instruments (#322) by @morrowrasmus
+* Utils: General improvements in plotutils
+* General: Dropped support for python 3.9 and added support for python 3.12 (and probably beyond) by upgrading `OtherPaths`
+* Bug fixes.
+
 ## 1.0.1
 
 * Utils: `example_data` now includes auto-download of example data

{cellpy-1.0.1.post3 → cellpy-1.0.2}/README.md

@@ -9,7 +9,7 @@
 
 This Python Package was developed to help the
 researchers at IFE, Norway, in their cumbersome task of
-interpreting and handling data from cycling tests of
+interpreting and handling data from cycling tests of batteries and cells.
 
 ## Features
 

{cellpy-1.0.1.post3 → cellpy-1.0.2}/cellpy/__init__.py

@@ -21,22 +21,27 @@ import logging
 import warnings
 
 import cellpy._version
+
+
 from cellpy.parameters import prms  # TODO: this might give circular ref
 from cellpy.parameters import prmreader
-from cellpy.readers import cellreader, dbreader, filefinder, do
-from cellpy.readers.core import Q, ureg
 
 __version__ = cellpy._version.__version__
 
+from cellpy.readers import cellreader, dbreader, filefinder, do
+
+# from cellpy.readers.core import Q, ureg
+
 logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 # TODO: (v2.0) remove this and enforce using for example `import cellpy.session as clp` and then
 #  run `prmreader.initialize` in that `__init__` instead:
-init = prmreader.initialize
+init = parameters.prmreader.initialize
 init()
 
 # TODO: (v2.0) remove this and enforce using `cellpy.get` (or `cellpy.cellreader.get`) instead:
 get = cellreader.get
+print_instruments = readers.cellreader.print_instruments
 
 __all__ = [
     "cellreader",
@@ -47,6 +52,6 @@ __all__ = [
     "get",
     "do",
     "init",
-    "ureg",
-    "Q",
+    # "ureg",
+    # "Q",
 ]

cellpy-1.0.2/cellpy/_version.py

@@ -0,0 +1 @@
+__version__ = "1.0.2"

{cellpy-1.0.1.post3 → cellpy-1.0.2}/cellpy/exceptions.py

@@ -25,6 +25,12 @@ class FileNotFound(Error):
     pass
 
 
+class SearchError(Error):
+    """Raised when the search function fails"""
+
+    pass
+
+
 class WrongFileVersion(Error):
     """Raised when the file version is wrong"""
 

cellpy-1.0.2/cellpy/internals/__init__.py

@@ -0,0 +1,10 @@
+from cellpy.libs.apipkg import initpkg
+
+initpkg(
+    __name__,
+    {
+        "externals": {
+            "fabric": "fabric",
+        },
+    },
+)

cellpy-1.0.2/cellpy/internals/core.py

@@ -0,0 +1,170 @@
+"""This module contains div classes etc that are not really connected to cellpy."""
+
+from dataclasses import dataclass
+import fnmatch
+import logging
+import os
+import pathlib
+import shutil
+import stat
+import sys
+import tempfile
+import time
+import warnings
+from typing import (
+    Any,
+    Tuple,
+    Dict,
+    List,
+    Union,
+    TypeVar,
+    Generator,
+    Optional,
+    Iterable,
+    Callable,
+    Type,
+    cast,
+)
+
+# import fabric
+from . import externals as externals
+from cellpy.exceptions import UnderDefined
+from cellpy.internals import otherpath
+from cellpy.internals.otherpath import (
+    URI_PREFIXES,
+    IMPLEMENTED_PROTOCOLS,
+    ENV_VAR_CELLPY_KEY_FILENAME,
+    ENV_VAR_CELLPY_PASSWORD,
+)
+
+OtherPath = otherpath.get_otherpath_class()
+
+
+def check_connection(
+    p=None,
+):
+    """Check if the connection works.
+
+    This is a helper function for cellpy v1.0 only and should be removed in later versions after
+    the OtherPath class has been updated to work with python >= 3.12.
+
+    Args:
+        p (str, pathlib.Path or OtherPath, optional): The path to check. Defaults to prms.Paths.rawdatadir.
+
+    """
+    # Note: users run this function from helpers.py
+    from pprint import pprint
+
+    logging.debug("checking connection")
+    if p is None:
+        print("No path given. Checking rawdatadir from prms.")
+
+        # need to import prms here to avoid circular imports:
+        from cellpy import prms
+
+        p = prms.Paths.rawdatadir
+
+    # recreating the OtherPath object to OtherPath since core is imported in the top __init__.py
+    # file resulting in isinstance(p, OtherPath) to be False
+    p = OtherPath(p)
+    logging.debug(f"p: {p}")
+
+    print("\nCollecting connection information:")
+
+    if not p.is_external:
+        print(f"   - {p} is not external. Returning.")
+        return {}
+
+    info = {
+        "is_external": p.is_external,
+        "uri_prefix": p.uri_prefix,
+        "location": p.location,
+        "raw_path": p.raw_path,
+        "full_path": p.full_path,
+        "host": p.location,
+    }
+
+    uri_prefix = p.uri_prefix.replace("//", "")
+    info["uri_prefix"] = uri_prefix
+    if uri_prefix not in URI_PREFIXES:
+        print(f"   - uri_prefix {uri_prefix} not recognized")
+    if uri_prefix not in IMPLEMENTED_PROTOCOLS:
+        print(f"   - uri_prefix {uri_prefix.replace(':', '')} not implemented yet")
+
+    password = os.getenv(ENV_VAR_CELLPY_PASSWORD, None)
+    info["password"] = "********" if password is not None else None
+
+    key_filename = os.getenv(ENV_VAR_CELLPY_KEY_FILENAME, None)
+    if password is None and key_filename is None:
+        print(
+            f"   - You must define either {ENV_VAR_CELLPY_PASSWORD} "
+            f"or {ENV_VAR_CELLPY_KEY_FILENAME} environment variables."
+        )
+    if key_filename is not None:
+        key_filename = pathlib.Path(key_filename).expanduser().resolve()
+        info["key_filename"] = str(key_filename)
+        if not pathlib.Path(key_filename).is_file():
+            print(f"   - Could not find key file {key_filename}")
+    else:
+        print("   - Using password")
+
+    for k, v in info.items():
+        print(f" {k}: {v}")
+
+    print("\nChecking connection:")
+    connect_kwargs, host = p.connection_info()
+
+    path_separator = "/"  # only supports unix-like systems
+    with externals.fabric.Connection(host, connect_kwargs=connect_kwargs) as conn:
+        try:
+            t1 = time.perf_counter()
+            try:
+                sftp_conn = conn.sftp()
+            except Exception as e:
+                print(f"   - Could not connect to {host}")
+                print(f"     {e}")
+                return info
+
+            print(f" connecting     [{time.perf_counter() - t1:.2f} seconds] OK")
+            sftp_conn.chdir(p.raw_path)
+            print(f" chdir          [{time.perf_counter() - t1:.2f} seconds] OK")
+            files = [
+                f"{p.raw_path}{path_separator}{f}"
+                for f in sftp_conn.listdir()
+                if not stat.S_ISDIR(sftp_conn.stat(f).st_mode)
+            ]
+            print(f" listing files  [{time.perf_counter() - t1:.2f} seconds] OK")
+            sub_dirs = [
+                f"{p.raw_path}{path_separator}{f}"
+                for f in sftp_conn.listdir()
+                if stat.S_ISDIR(sftp_conn.stat(f).st_mode)
+            ]
+            n_files = len(files)
+            n_sub_dirs = len(sub_dirs)
+            info["number_of_files"] = n_files
+            info["number_of_sub_directories"] = n_sub_dirs
+            print(f" found {n_files} files and {n_sub_dirs} sub directories")
+
+        except FileNotFoundError as e:
+            print(
+                f"   - FileNotFoundError: Could not perform directory listing in {p.raw_path} on {host}." f"\n     {e}"
+            )
+
+    return info
+
+
+def _check():
+    print("Testing OtherPath-connection")
+    # info = check_connection()
+    p0 = "scp://odin/home/jepe@ad.ife.no/projects"
+    # info = check_connection(p0)
+    p1 = "scp://odin/home/jepe@ad.ife.no/this-folder-does-not-exist"
+    # info = check_connection(p1)
+    p2 = pathlib.Path(".").resolve()
+    info = check_connection(p2)
+
+
+if __name__ == "__main__":
+    print("------------------")
+    logging.debug("testing OtherPath")
+    _check()