cellpy 0.4.2.post4__tar.gz → 0.4.2.post6__tar.gz

{cellpy-0.4.2.post4 → cellpy-0.4.2.post6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellpy
-Version: 0.4.2.post4
+Version: 0.4.2.post6
 Summary: Extract and manipulate data from battery cell testers.
 Home-page: https://github.com/jepegit/cellpy
 Author: Jan Petter Maehlen

cellpy-0.4.2.post6/cellpy/_version.py

@@ -0,0 +1 @@
+__version__ = "0.4.2post6"

{cellpy-0.4.2.post4 → cellpy-0.4.2.post6}/cellpy/log.py

@@ -1,141 +1,141 @@
-"""Set up logger instance"""
-
-import datetime
-import json
-import logging
-import logging.config
-import os
-import pathlib
-import shutil
-import tempfile
-import warnings
-
-from cellpy import prms
-
-logging.raiseExceptions = False
-
-
-def setup_logging(
-    default_json_path=None,
-    default_level=None,
-    env_key="LOG_CFG",
-    custom_log_dir=None,
-    reset_big_log=False,
-    max_size=5_000_000,
-    testing=False,
-):
-    """Setup logging configuration.
-
-    Args:
-        default_level: default log-level to screen (std.out).
-        default_json_path: path to config file for setting up logging.
-        env_key (str): use this environment prm to try to get default_json_path.
-        custom_log_dir: path for saving logs.
-        reset_big_log (bool): reset log if too big (max_size).
-        max_size (int): if reset_log, this is the max limit.
-        testing (bool): set as True if testing, and you don't want to create any .log files
-
-    """
-
-    if not default_json_path:
-        default_json_path = os.path.join(
-            os.path.dirname(os.path.realpath(__file__)), "logging.json"
-        )
-    path = default_json_path
-    value = os.getenv(env_key, None)
-    if value:
-        path = value
-
-    if default_level is None:
-        default_level = "CRITICAL"
-
-    # loading logging configs
-    if os.path.exists(path):
-        with open(path, "rt") as f:
-            config = json.load(f)
-
-        if testing:
-            log_dir = tempfile.mkdtemp()
-        elif custom_log_dir:
-            log_dir = custom_log_dir
-        else:
-            log_dir = os.path.abspath(prms.Paths.filelogdir)
-
-        if not os.path.isdir(log_dir):
-            warning_txt = (
-                "\nCould not set custom log-dir - "
-                "non-existing directory"
-                f"\nDir: {log_dir}"
-                "\nUsing current directory instead: "
-                f"{os.getcwd()}"
-            )
-            logging.warning(warning_txt)
-            log_dir = os.getcwd()
-
-        for file_handler in [
-            "error_file_handler",
-            "info_file_handler",
-            "debug_file_handler",
-        ]:
-            try:
-                file_name = config["handlers"][file_handler]["filename"]
-                logging.debug("Setting file handlers for logging.")
-                logging.debug(f"Filename: {file_name}")
-                logging.debug(f"Full path: {os.path.join(log_dir,file_name)}")
-                # print(f"Filename: {file_name}")
-                # print(f"Full path: {os.path.join(log_dir,file_name)}")
-                config["handlers"][file_handler]["filename"] = os.path.join(
-                    log_dir, file_name
-                )
-
-                if reset_big_log:
-                    full_log_file_path = pathlib.Path(log_dir) / file_name
-                    if full_log_file_path.is_file():
-                        file_size = full_log_file_path.lstat().st_size
-                        if file_size > max_size:
-                            d_str = datetime.datetime.now().strftime("%Y_%m_%d_%H_%M")
-                            new_file_name = "_".join([d_str, file_name])
-                            new_full_log_file_path = (
-                                pathlib.Path(log_dir) / new_file_name
-                            )
-                            shutil.copy(full_log_file_path, new_full_log_file_path)
-                    else:
-                        logging.debug(
-                            "Could not reset big log: could not find the file"
-                        )
-
-            except Exception as e:
-                warnings.warn("\nCould not set custom log-dir" + str(e))
-
-        if default_level:
-            w_txt = "\nCould not set custom default level for logger"
-            if default_level not in [
-                "INFO",
-                "DEBUG",
-                "CRITICAL",
-                logging.INFO,
-                logging.DEBUG,
-                logging.CRITICAL,
-            ]:
-                _txt = "\nonly 'INFO', 'DEBUG' and 'CRITICAL' is supported"
-                _txt += " as default_level"
-                warnings.warn(w_txt + _txt)
-
-            else:
-                try:
-                    config["handlers"]["console"]["level"] = default_level
-                    if default_level in ["DEBUG", logging.DEBUG]:
-                        config["handlers"]["console"]["formatter"] = "stamped"
-
-                except Exception as e:
-                    warnings.warn(w_txt + "\n" + str(e))
-
-        logging.config.dictConfig(config)
-    else:
-        if not default_level:
-            default_level = logging.CRITICAL
-        logging.basicConfig(level=default_level)
-
-
-if __name__ == "__main__":
-    setup_logging()
+"""Set up logger instance"""
+
+import datetime
+import json
+import logging
+import logging.config
+import os
+import pathlib
+import shutil
+import tempfile
+import warnings
+
+from cellpy import prms
+
+logging.raiseExceptions = False
+
+
+def setup_logging(
+    default_json_path=None,
+    default_level=None,
+    env_key="LOG_CFG",
+    custom_log_dir=None,
+    reset_big_log=False,
+    max_size=5_000_000,
+    testing=False,
+):
+    """Setup logging configuration.
+
+    Args:
+        default_level: default log-level to screen (std.out).
+        default_json_path: path to config file for setting up logging.
+        env_key (str): use this environment prm to try to get default_json_path.
+        custom_log_dir: path for saving logs.
+        reset_big_log (bool): reset log if too big (max_size).
+        max_size (int): if reset_log, this is the max limit.
+        testing (bool): set as True if testing, and you don't want to create any .log files
+
+    """
+
+    if not default_json_path:
+        default_json_path = os.path.join(
+            os.path.dirname(os.path.realpath(__file__)), "logging.json"
+        )
+    path = default_json_path
+    value = os.getenv(env_key, None)
+    if value:
+        path = value
+
+    if default_level is None:
+        default_level = "CRITICAL"
+
+    # loading logging configs
+    if os.path.exists(path):
+        with open(path, "rt") as f:
+            config = json.load(f)
+
+        if testing:
+            log_dir = tempfile.mkdtemp()
+        elif custom_log_dir:
+            log_dir = custom_log_dir
+        else:
+            log_dir = os.path.abspath(prms.Paths.filelogdir)
+
+        if not os.path.isdir(log_dir):
+            warning_txt = (
+                "\nCould not set custom log-dir - "
+                "non-existing directory"
+                f"\nDir: {log_dir}"
+                "\nUsing current directory instead: "
+                f"{os.getcwd()}"
+            )
+            logging.warning(warning_txt)
+            log_dir = os.getcwd()
+
+        for file_handler in [
+            "error_file_handler",
+            "info_file_handler",
+            "debug_file_handler",
+        ]:
+            try:
+                file_name = config["handlers"][file_handler]["filename"]
+                logging.debug("Setting file handlers for logging.")
+                logging.debug(f"Filename: {file_name}")
+                logging.debug(f"Full path: {os.path.join(log_dir,file_name)}")
+                # print(f"Filename: {file_name}")
+                # print(f"Full path: {os.path.join(log_dir,file_name)}")
+                config["handlers"][file_handler]["filename"] = os.path.join(
+                    log_dir, file_name
+                )
+
+                if reset_big_log:
+                    full_log_file_path = pathlib.Path(log_dir) / file_name
+                    if full_log_file_path.is_file():
+                        file_size = full_log_file_path.lstat().st_size
+                        if file_size > max_size:
+                            d_str = datetime.datetime.now().strftime("%Y_%m_%d_%H_%M")
+                            new_file_name = "_".join([d_str, file_name])
+                            new_full_log_file_path = (
+                                pathlib.Path(log_dir) / new_file_name
+                            )
+                            shutil.copy(full_log_file_path, new_full_log_file_path)
+                    else:
+                        logging.debug(
+                            "Could not reset big log: could not find the file"
+                        )
+
+            except Exception as e:
+                warnings.warn("\nCould not set custom log-dir" + str(e))
+
+        if default_level:
+            w_txt = "\nCould not set custom default level for logger"
+            if default_level not in [
+                "INFO",
+                "DEBUG",
+                "CRITICAL",
+                logging.INFO,
+                logging.DEBUG,
+                logging.CRITICAL,
+            ]:
+                _txt = "\nonly 'INFO', 'DEBUG' and 'CRITICAL' is supported"
+                _txt += " as default_level"
+                warnings.warn(w_txt + _txt)
+
+            else:
+                try:
+                    config["handlers"]["console"]["level"] = default_level
+                    if default_level in ["DEBUG", logging.DEBUG]:
+                        config["handlers"]["console"]["formatter"] = "stamped"
+
+                except Exception as e:
+                    warnings.warn(w_txt + "\n" + str(e))
+
+        logging.config.dictConfig(config)
+    else:
+        if not default_level:
+            default_level = logging.CRITICAL
+        logging.basicConfig(level=default_level)
+
+
+if __name__ == "__main__":
+    setup_logging()

{cellpy-0.4.2.post4 → cellpy-0.4.2.post6}/cellpy/readers/instruments/arbin_res.py

@@ -550,7 +550,7 @@ class DataLoader(BaseLoader):
         # --------- read global-data ------------------------------------
         self.logger.debug("reading global data table")
         sql = "select * from %s" % table_name_global
-        global_data_df = pd.read_sql_query(sql, conn)
+        global_data_df = pd.read_sql_query(sql=sa.text(sql), con=conn.connect())
         # col_names = list(global_data_df.columns.values)
         self.logger.debug("sql statement: %s" % sql)
 
@@ -595,7 +595,7 @@ class DataLoader(BaseLoader):
             sql_4 = "AND %s=%i " % (cycle_txt, cycle_number)
             sql = sql_1 + sql_2 + sql_3 + sql_4 + sql_5
             self.logger.debug("sql statement: %s" % sql)
-            normal_df = pd.read_sql_query(sql, conn)
+            normal_df = pd.read_sql_query(sql=sa.text(sql), con=conn.connect())
             t2 = time.time()
             dt = t2 - t1
             self.logger.debug("time: %f" % dt)
@@ -659,7 +659,7 @@ class DataLoader(BaseLoader):
         # --------- read global-data ------------------------------------
         self.logger.debug("reading global data table")
         sql = "select * from %s" % table_name_global
-        global_data_df = pd.read_sql_query(sql, conn)
+        global_data_df = pd.read_sql_query(sql=sa.text(sql), con=conn.connect())
         # col_names = list(global_data_df.columns.values)
         self.logger.debug("sql statement: %s" % sql)
 
@@ -701,7 +701,7 @@ class DataLoader(BaseLoader):
             sql_4 = "AND %s=%i " % (cycle_txt, cycle_number)
             sql = sql_1 + sql_2 + sql_3 + sql_4 + sql_5
             self.logger.debug("sql statement: %s" % sql)
-            normal_df = pd.read_sql_query(sql, conn)
+            normal_df = pd.read_sql_query(sql=sa.text(sql), con=conn.connect())
             t2 = time.time()
             dt = t2 - t1
             self.logger.debug("time: %f" % dt)
@@ -761,7 +761,7 @@ class DataLoader(BaseLoader):
         if sql is None:
             sql = f"select * from {table_name}"
         self.logger.debug(f"sql statement: {sql}")
-        df = pd.read_sql_query(sql, conn)
+        df = pd.read_sql_query(sql=sa.text(sql), con=conn.connect())
         return df
 
     def _make_name_from_frame(self, df, aux_index, data_type, dx_dt=False):
@@ -849,7 +849,7 @@ class DataLoader(BaseLoader):
                 data.test_ID,
                 self.arbin_headers_normal.data_point_txt,
             )
-            summary_df = pd.read_sql_query(sql, conn)
+            summary_df = pd.read_sql_query(sql=sa.text(sql), con=conn.connect())
 
             if summary_df.empty and prms.Reader.use_cellpy_stat_file:
                 txt = "\nCould not find any summary (stats-file)!"
@@ -1397,14 +1397,13 @@ class DataLoader(BaseLoader):
         if not prms.Instruments.Arbin.chunk_size:
             self.logger.debug("no chunk-size given")
             # memory here
-            normal_df = pd.read_sql_query(sql, conn)
+            normal_df = pd.read_sql_query(sql=sa.text(sql), con=conn.connect())
             # memory here
             length_of_test = normal_df.shape[0]
         else:
             self.logger.debug(f"chunk-size: {prms.Instruments.Arbin.chunk_size}")
             self.logger.debug("creating a pd.read_sql_query generator")
-            normal_df_reader = pd.read_sql_query(
-                sql, conn, chunksize=prms.Instruments.Arbin.chunk_size
+            normal_df_reader = pd.read_sql_query(sql=sa.text(sql), con=conn.connect(), chunksize=prms.Instruments.Arbin.chunk_size
             )
             normal_df = None
             chunk_number = 0

{cellpy-0.4.2.post4 → cellpy-0.4.2.post6}/cellpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellpy
-Version: 0.4.2.post4
+Version: 0.4.2.post6
 Summary: Extract and manipulate data from battery cell testers.
 Home-page: https://github.com/jepegit/cellpy
 Author: Jan Petter Maehlen

{cellpy-0.4.2.post4 → cellpy-0.4.2.post6}/cellpy.egg-info/SOURCES.txt

@@ -84,6 +84,7 @@ cellpy/utils/batch_tools/engines.py
 cellpy/utils/data/20160805_test001_45_cc.h5
 cellpy/utils/data/raw/20160805_test001_45_cc_01.res
 docs/Makefile
+docs/adapted_readme.rst
 docs/authors.rst
 docs/basics.rst
 docs/conf.py
@@ -96,18 +97,25 @@ docs/index.rst
 docs/installation.rst
 docs/make.bat
 docs/notebooks.rst
-docs/readme.rst
 docs/tips_and_tricks.rst
 docs/usage.rst
 docs/utils.rst
-docs/_build/.doctrees/nbsphinx/notebooks_tutorial_get_cap_6_0.png
-docs/_build/.doctrees/nbsphinx/notebooks_tutorial_get_cap_7_0.png
-docs/_build/.doctrees/nbsphinx/notebooks_tutorial_get_cap_8_0.png
-docs/_build/.doctrees/nbsphinx/notebooks_tutorial_simple_plot_2_0.png
-docs/_build/_images/notebooks_tutorial_get_cap_6_0.png
-docs/_build/_images/notebooks_tutorial_get_cap_7_0.png
-docs/_build/_images/notebooks_tutorial_get_cap_8_0.png
-docs/_build/_images/notebooks_tutorial_simple_plot_2_0.png
+docs/_build/.doctrees/nbsphinx/examples_and_tutorials_notebooks_tutorial_get_cap_6_0.png
+docs/_build/.doctrees/nbsphinx/examples_and_tutorials_notebooks_tutorial_get_cap_7_0.png
+docs/_build/.doctrees/nbsphinx/examples_and_tutorials_notebooks_tutorial_get_cap_8_0.png
+docs/_build/.doctrees/nbsphinx/examples_and_tutorials_notebooks_tutorial_simple_plot_2_0.png
+docs/_build/_images/examples_and_tutorials_notebooks_tutorial_get_cap_6_0.png
+docs/_build/_images/examples_and_tutorials_notebooks_tutorial_get_cap_7_0.png
+docs/_build/_images/examples_and_tutorials_notebooks_tutorial_get_cap_8_0.png
+docs/_build/_images/examples_and_tutorials_notebooks_tutorial_simple_plot_2_0.png
+docs/_build/_images/graphviz-22185705e237fa530df24e4af50cb25833165e25.png
+docs/_build/_images/graphviz-246f2486cd940f2ea40a07f847c86c22b2607ca8.png
+docs/_build/_images/graphviz-42e9bc826d476a3d361a7f410e989ed34dc1aa85.png
+docs/_build/_images/graphviz-619216a42370fd49669c083549129b8470c8fae1.png
+docs/_build/_images/graphviz-6deb64a460668e8ef9bf0ca653314119adeeae66.png
+docs/_build/_images/graphviz-83b62e03ef369ff0a30f027892dba95b91ea8b6c.png
+docs/_build/_images/graphviz-ce8a9fe2ba01194aed847e0248d749db4093aca1.png
+docs/_build/_images/graphviz-e94a5352318e02fcc5ef1f813e02a526c39af791.png
 docs/_build/_images/templates_jupyterlab_001.png
 docs/_build/_images/tutorials_utils_plotting_fig1.png
 docs/_build/_images/tutorials_utils_plotting_fig2.png

cellpy-0.4.2.post6/docs/adapted_readme.rst

@@ -0,0 +1,57 @@
+==================================
+Welcome to cellpy's documentation!
+==================================
+
+ - *a library for assisting in analysing batteries and cells*
+
+
+.. image:: https://img.shields.io/pypi/v/cellpy.svg
+        :target: https://pypi.python.org/pypi/cellpy
+
+.. image:: https://img.shields.io/travis/jepegit/cellpy.svg
+        :target: https://travis-ci.org/jepegit/cellpy
+
+.. image:: https://readthedocs.org/projects/cellpy/badge/?version=latest
+        :target: https://cellpy.readthedocs.io/en/latest/?badge=latest
+        :alt: Documentation Status
+
+.. image:: https://pepy.tech/badge/cellpy
+        :target: https://pepy.tech/project/cellpy
+
+
+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
+batteries and cells.
+
+|ProjectVersion|
+
+Installation and dependencies
+-----------------------------
+
+The easiest way to install ``cellpy`` is to install with conda or pip.
+
+With conda::
+
+   conda install -c conda-forge cellpy
+
+Or if you prefer installing using pip::
+
+   python -m pip install cellpy
+
+Have a look at the documentation for more detailed installation procedures, especially
+with respect to "difficult" dependencies when installing with pip.
+
+Licence
+-------
+
+``cellpy`` is free software made available under the MIT License.
+
+Features
+--------
+
+* Load test-data and store in a common format.
+* Summarize and compare data.
+* Filter out the steps of interest.
+* Process and plot the data.
+* And more...