Merge pull request #17 from TimChild/2023_EndOfCDTidy

.gitignore

@@ -25,3 +25,5 @@ tests/temp.h5
 config.toml
 tests/new_dat/test_config.toml
 tests/fixtures/.config.toml
+
+build/

requirements.txt

@@ -1,135 +1,162 @@
-algopy==0.5.7
-anyio==3.6.1
+aiofiles==22.1.0
+aiosqlite==0.18.0
+ansi2html==1.8.0
+anyio==3.6.2
 argon2-cffi==21.3.0
 argon2-cffi-bindings==21.2.0
-asteval==0.9.27
-asttokens==2.0.5
-attrs==21.4.0
-Babel==2.10.3
+arrow==1.2.3
+asteval==0.9.29
+asttokens==2.2.1
+attrs==22.2.0
+Babel==2.12.1
 backcall==0.2.0
-beautifulsoup4==4.11.1
-bleach==5.0.1
-Brotli==1.0.9
+beautifulsoup4==4.12.0
+black==23.1.0
+bleach==6.0.0
 cachelib==0.9.0
-certifi @ file:///C:/Windows/TEMP/abs_e9b7158a-aa56-4a5b-87b6-c00d295b01fanefpc8_o/croots/recipe/certifi_1655968940823/work/certifi
+certifi @ file:///C:/b/abs_85o_6fm0se/croot/certifi_1671487778835/work/certifi
 cffi==1.15.1
-charset-normalizer==2.1.0
+charset-normalizer==3.1.0
 click==8.1.3
-colorama==0.4.5
+colorama==0.4.6
+comm==0.1.3
+contourpy==1.0.7
 cycler==0.11.0
-dacite==1.6.0
-dash==2.6.0
-dash-bootstrap-components==1.2.0
+dash==2.9.1
+dash-bootstrap-components==1.4.1
 dash-core-components==2.0.0
--e git+https://github.com/TimChild/dash_data_viewer.git@421424acee527b396b5b9d55e67b6d0444538a89#egg=dash_data_viewer
-dash-extensions==0.0.65
+dash-extensions==0.1.13
 dash-html-components==2.0.0
-dash-labs==1.1.0
 dash-table==5.0.0
--e git+https://github.com/TimChild/dat_analysis.git@fc3c8d5e9c5a0f3e2e9c3182857439c95f15cebe#egg=dat_analysis
-debugpy==1.6.2
+dat-analysis @ file:///D:/GitHub/dat_analysis
+debugpy==1.6.6
 decorator==5.1.1
 defusedxml==0.7.1
 deprecation==2.1.0
-dictor==0.1.10
+dictor==0.1.11
 EditorConfig==0.12.3
-entrypoints==0.4
-executing==0.8.3
-fastjsonschema==2.16.1
-filelock==3.7.1
-Flask==2.1.2
-Flask-Caching==2.0.0
-Flask-Compress==1.12
-fonttools==4.34.4
-future==0.18.2
-h5py==3.7.0
-idna==3.3
+executing==1.2.0
+fastjsonschema==2.16.3
+filelock==3.10.7
+Flask==2.2.3
+Flask-Caching==2.0.2
+fonttools==4.39.3
+fqdn==1.5.1
+future==0.18.3
+h5py==3.8.0
+idna==3.4
 igorwriter==0.3.0
-ipykernel==6.15.1
-ipython==8.4.0
+ipykernel==6.22.0
+ipython==8.11.0
 ipython-genutils==0.2.0
-ipywidgets==7.7.1
+ipywidgets==8.0.6
+isoduration==20.11.0
 itsdangerous==2.1.2
-jedi==0.18.1
+jedi==0.18.2
 Jinja2==3.1.2
-jsbeautifier==1.14.4
-json5==0.9.9
-jsonschema==4.7.2
+jsbeautifier==1.14.7
+json5==0.9.11
+jsonpointer==2.3
+jsonschema==4.17.3
 jupyter==1.0.0
-jupyter-client==7.3.4
-jupyter-console==6.4.4
-jupyter-core==4.11.1
-jupyter-server==1.18.1
-jupyterlab==3.4.5
+jupyter-console==6.6.3
+jupyter-contrib-core==0.4.2
+jupyter-contrib-nbextensions==0.7.0
+jupyter-dash==0.4.2
+jupyter-events==0.6.3
+jupyter-highlight-selected-word==0.2.0
+jupyter-nbextensions-configurator==0.6.1
+jupyter-ydoc==0.2.3
+jupyter_client==8.1.0
+jupyter_core==5.3.0
+jupyter_server==2.5.0
+jupyter_server_fileid==0.8.0
+jupyter_server_terminals==0.4.4
+jupyter_server_ydoc==0.8.0
+jupyterlab==3.6.2
 jupyterlab-pygments==0.2.2
-jupyterlab-server==2.15.0
-jupyterlab-vim==0.15.1
-jupyterlab-widgets==1.1.1
+jupyterlab-widgets==3.0.7
+jupyterlab_server==2.21.0
 kaleido==0.2.1
 kiwisolver==1.4.4
-lmfit==1.0.3
-MarkupSafe==2.1.1
-matplotlib==3.5.2
-matplotlib-inline==0.1.3
-mistune==0.8.4
-more-itertools==8.13.0
-nbclassic==0.4.3
-nbclient==0.6.6
-nbconvert==6.5.1
-nbformat==5.4.0
-nest-asyncio==1.5.5
-notebook==6.4.12
-notebook-shim==0.1.0
-numdifftools==0.9.40
-numpy==1.23.1
-opencv-python==4.6.0.66
-packaging==21.3
-pandas==1.4.3
+lmfit==1.1.0
+lxml==4.9.2
+MarkupSafe==2.1.2
+matplotlib==3.7.1
+matplotlib-inline==0.1.6
+mistune==2.0.5
+more-itertools==9.1.0
+mypy-extensions==1.0.0
+nb-black==1.0.7
+nbclassic==0.5.3
+nbclient==0.7.2
+nbconvert==7.2.10
+nbformat==5.8.0
+nest-asyncio==1.5.6
+nodejs-bin==18.4.0a4
+nodejs-cmd==0.0.1a0
+notebook==6.5.3
+notebook_shim==0.2.2
+numdifftools==0.9.41
+numpy==1.24.2
+opencv-python==4.7.0.72
+packaging==23.0
+pandas==1.5.3
 pandocfilters==1.5.0
 parso==0.8.3
-patsy==0.5.2
+pathspec==0.11.1
 pickleshare==0.7.5
-Pillow==9.3.0
-plotly==5.9.0
-progressbar==2.5
-progressbar2==4.0.0
-prometheus-client==0.14.1
-prompt-toolkit==3.0.30
-psutil==5.9.1
+Pillow==9.4.0
+platformdirs==3.2.0
+plotly==5.13.1
+prometheus-client==0.16.0
+prompt-toolkit==3.0.38
+psutil==5.9.4
 pure-eval==0.2.2
 pycparser==2.21
-Pygments==2.12.0
+Pygments==2.14.0
 pyparsing==3.0.9
-pyrsistent==0.18.1
+pyrsistent==0.19.3
 python-dateutil==2.8.2
-python-utils==3.3.3
-pytz==2022.1
-pywin32==304
-pywinpty==2.0.6
-pyzmq==23.2.0
-qtconsole==5.3.1
-QtPy==2.1.0
-requests==2.28.1
-scipy==1.8.1
+python-json-logger==2.0.7
+python-slugify==8.0.1
+pytz==2023.2
+pywin32==306
+pywinpty==2.0.10
+PyYAML==6.0
+pyzmq==25.0.2
+qtconsole==5.4.1
+QtPy==2.3.0
+requests==2.28.2
+retrying==1.3.4
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+scipy==1.10.1
 Send2Trash==1.8.0
 singleton-decorator==1.0.0
 six==1.16.0
-slugify==0.0.1
-sniffio==1.2.0
-soupsieve==2.3.2.post1
-stack-data==0.3.0
-statsmodels==0.13.2
-tenacity==8.0.1
-terminado==0.15.0
-tinycss2==1.1.1
+sniffio==1.3.0
+soupsieve==2.4
+stack-data==0.6.2
+tdqm==0.0.1
+tenacity==8.2.2
+terminado==0.17.1
+text-unidecode==1.3
+tinycss2==1.2.1
 toml==0.10.2
+tomli==2.0.1
 tornado==6.2
-traitlets==5.3.0
+tqdm==4.65.0
+traitlets==5.9.0
 uncertainties==3.1.7
-urllib3==1.26.11
-wcwidth==0.2.5
+uri-template==1.2.0
+urllib3==1.26.15
+wcwidth==0.2.6
+webcolors==1.13
 webencodings==0.5.1
-websocket-client==1.3.3
-Werkzeug==2.1.2
-widgetsnbextension==3.6.1
+websocket-client==1.5.1
+Werkzeug==2.2.3
+widgetsnbextension==4.0.7
 wincertstore==0.2
+y-py==0.5.9
+ypy-websocket==0.8.2

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='dat_analysis',
-    version='3.1.2',
+    version='3.2.0',
     url='https://github.com/TimChild/dat_analysis',
     license='MIT',
     author='Tim Child',
@@ -28,7 +28,7 @@
         'scipy',
         'pillow',
         'deprecation',
-        'slugify',
+        'python-slugify',
         'igorwriter',
         'singleton_decorator',
         'numdifftools',  # For lmfit uncertainties on powell method
@@ -37,7 +37,13 @@
         'jupyter',  # Only here because it is so often useful in the environment
         'jupyter_contrib_nbextensions',  # For exporting jupyter notebooks to pdf
         'jupyterlab',  # Only here because it is so often useful in the environment
-        'progressbar2',  # Often useful when working with large datasets
+        'tdqm',  # Progressbar often useful when working with large datasets
         'opencv-python',  # For shift_tracker_algorithm (import cv2)
+        'nb_black',  # For formatting jupyter files with %load_ext lab_black
+        'dash>2.0',  # For making interactive dash apps
+        'jupyter-dash',  # Enables dash apps to work in jupyter without blocking cells
+        'nodejs-bin[cmd]>=14',  # Node>14 required for 'jupyter lab build' after installing jupyter-dash
+        'dash-bootstrap-components',
+        'dash-extensions',  # Provides ServersideOutput among many other things
     ]
 )

src/dat_analysis/__init__.py

@@ -1,8 +1,7 @@
-# from .dat_object.make_dat import get_dat, get_dats
-# from .dat.dat_util import get_local_config
-from .dat.dat_hdf import get_dat, get_dat_from_exp_filepath
+"""This sets up what is accessible directly from dat_analysis.
+
+This should be reserved for VERY commonly used functions ONLY
 
-# try:
-#     config = get_local_config()
-# except RuntimeError as e:
-#     config = None
+E.g. from dat_analysis import get_dat will work and the user doesn't need to know that it's tucked away in dat_analysis.dat.dat_hdf
+"""
+from .dat.dat_hdf import get_dat, get_dat_from_exp_filepath