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Hatoris / BioPlate

A simple application to generate annotated plates used in biological experiments
https://hatoris.github.io/BioPlate/
MIT License
7 stars 1 forks source link

Additional arguments should be named <dialectname>_<argument>, got 'useexisting' #3

Open ajasja opened 1 year ago

ajasja commented 1 year ago

Hi,

Just running the simple example 

from BioPlate import BioPlate
simple_plate = BioPlate(12, 8)
simple_plate.set("A1", "test1")
simple_plate["A1"] = "test1"

gives the error:

c:\bin\python\anaconda64\envs\spectraplotpy\lib\site-packages\BioPlate\database\plate_db.py:7: SAWarning: This declarative base already contains a class with the same class name and module name as BioPlate.database.plate_db.PlateDatabase, and will be replaced in the string-lookup table.
  class PlateDatabase(Database.Base):
Output exceeds the [size limit](command:workbench.action.openSettings?[). Open the full output data [in a text editor](command:workbench.action.openLargeOutput?791d103c-2651-4ae3-a296-c72ddf806d00)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
d:\owncloud\Projekti_KI\SIDE\2022-09-29__ph_FRET\2022-10-17__plate_reading.ipynb Cell 2 in <cell line: 1>()
----> [1](vscode-notebook-cell:/d%3A/owncloud/Projekti_KI/SIDE/2022-09-29__ph_FRET/2022-10-17__plate_reading.ipynb#X14sZmlsZQ%3D%3D?line=0) from BioPlate import BioPlate
      [2](vscode-notebook-cell:/d%3A/owncloud/Projekti_KI/SIDE/2022-09-29__ph_FRET/2022-10-17__plate_reading.ipynb#X14sZmlsZQ%3D%3D?line=1) simple_plate = BioPlate(12, 8)
      [3](vscode-notebook-cell:/d%3A/owncloud/Projekti_KI/SIDE/2022-09-29__ph_FRET/2022-10-17__plate_reading.ipynb#X14sZmlsZQ%3D%3D?line=2) simple_plate.set("A1", "test1")

File c:\bin\python\anaconda64\envs\spectraplotpy\lib\site-packages\BioPlate\__init__.py:1, in <module>
----> 1 from BioPlate.bioplate import BioPlate

File c:\bin\python\anaconda64\envs\spectraplotpy\lib\site-packages\BioPlate\bioplate.py:16, in <module>
      1 from typing import (
      2     Dict,
      3     List,
   (...)
     11     ClassVar,
     12 )
     14 from collections import OrderedDict
---> 16 from BioPlate.plate import Plate
     17 from BioPlate.inserts import Inserts
     18 from BioPlate.stack import Stack

File c:\bin\python\anaconda64\envs\spectraplotpy\lib\site-packages\BioPlate\plate.py:17, in <module>
     13 import numpy as np 
     15 from collections import OrderedDict
...
    427     )
    428 dialect_name, arg_name = m.group(1, 2)
    430 try:

TypeError: Additional arguments should be named <dialectname>_<argument>, got 'useexisting'

Env info (windows, python 3.10): 

 conda list
# packages in environment at C:\bin\python\anaconda64\envs\spectraplotpy:
#
# Name                    Version                   Build  Channel
arrow                     1.2.3                    pypi_0    pypi
asttokens                 2.0.5              pyhd3eb1b0_0
backcall                  0.2.0              pyhd3eb1b0_0
bioplate                  0.1.4                    pypi_0    pypi
blas                      1.0                         mkl
bottleneck                1.3.5           py310h9128911_0
brotli                    1.0.9                h2bbff1b_7
brotli-bin                1.0.9                h2bbff1b_7
bzip2                     1.0.8                he774522_0
ca-certificates           2022.07.19           haa95532_0
certifi                   2022.9.24       py310haa95532_0
chardet                   5.0.0                    pypi_0    pypi
colorama                  0.4.5           py310haa95532_0
colorcet                  3.0.1                    pypi_0    pypi
cycler                    0.11.0             pyhd3eb1b0_0
debugpy                   1.5.1           py310hd77b12b_0
decorator                 5.1.1              pyhd3eb1b0_0
docopt                    0.6.2                    pypi_0    pypi
entrypoints               0.4             py310haa95532_0
et-xmlfile                1.1.0                    pypi_0    pypi
executing                 0.8.3              pyhd3eb1b0_0
fftw                      3.3.9                h2bbff1b_1
fonttools                 4.37.4                   pypi_0    pypi
freetype                  2.10.4               hd328e21_0
glib                      2.69.1               h5dc1a3c_1
greenlet                  1.1.3.post0              pypi_0    pypi
gst-plugins-base          1.18.5               h9e645db_0
gstreamer                 1.18.5               hd78058f_0
icc_rt                    2022.1.0             h6049295_2
icu                       58.2                 ha925a31_3
inform                    1.27.0                   pypi_0    pypi
intel-openmp              2021.4.0          haa95532_3556
ipykernel                 6.15.2          py310haa95532_0
ipython                   8.4.0           py310haa95532_0
jedi                      0.18.1          py310haa95532_1
jpeg                      9e                   h2bbff1b_0
jupyter_client            7.3.5           py310haa95532_0
jupyter_core              4.11.1          py310haa95532_0
kiwisolver                1.4.2           py310hd77b12b_0
lerc                      3.0                  hd77b12b_0
libbrotlicommon           1.0.9                h2bbff1b_7
libbrotlidec              1.0.9                h2bbff1b_7
libbrotlienc              1.0.9                h2bbff1b_7
libclang                  12.0.0          default_h627e005_2
libdeflate                1.8                  h2bbff1b_5
libffi                    3.4.2                hd77b12b_4
libiconv                  1.16                 h2bbff1b_2
libogg                    1.3.5                h2bbff1b_1
libpng                    1.6.37               h2a8f88b_0
libsodium                 1.0.18               h62dcd97_0
libtiff                   4.4.0                h8a3f274_0
libvorbis                 1.3.7                he774522_0
libwebp                   1.2.4                h2bbff1b_0
libwebp-base              1.2.4                h2bbff1b_0
libxml2                   2.9.14               h0ad7f3c_0
libxslt                   1.1.35               h2bbff1b_0
lml                       0.1.0                    pypi_0    pypi
lz4-c                     1.9.3                h2bbff1b_1
matplotlib                3.5.2           py310haa95532_0
matplotlib-base           3.5.2           py310hd77b12b_0
matplotlib-inline         0.1.6           py310haa95532_0
mkl                       2021.4.0           haa95532_640
mkl-service               2.4.0           py310h2bbff1b_0
mkl_fft                   1.3.1           py310ha0764ea_0
mkl_random                1.2.2           py310h4ed8f06_0
munkres                   1.1.4                      py_0
nest-asyncio              1.5.5           py310haa95532_0
numexpr                   2.8.3           py310hb57aa6b_0
numpy                     1.23.1          py310h6d2d95c_0
numpy-base                1.23.1          py310h206c741_0
openpyxl                  3.0.10                   pypi_0    pypi
openssl                   1.1.1q               h2bbff1b_0
packaging                 21.3               pyhd3eb1b0_0
pandas                    1.4.4           py310hd77b12b_0
param                     1.12.2                   pypi_0    pypi
parso                     0.8.3              pyhd3eb1b0_0
pathlib                   1.0.1                    pypi_0    pypi
pcre                      8.45                 hd77b12b_0
pickleshare               0.7.5           pyhd3eb1b0_1003
pillow                    9.2.0           py310hdc2b20a_1
pip                       22.2.2          py310haa95532_0
ply                       3.11            py310haa95532_0
prompt-toolkit            3.0.20             pyhd3eb1b0_0
psutil                    5.9.0           py310h2bbff1b_0
pure_eval                 0.2.2              pyhd3eb1b0_0
pyct                      0.4.8                    pypi_0    pypi
pyexcel                   0.7.0                    pypi_0    pypi
pyexcel-io                0.6.6                    pypi_0    pypi
pyexcel-xls               0.7.0                    pypi_0    pypi
pyexcel-xlsx              0.6.0                    pypi_0    pypi
pygments                  2.11.2             pyhd3eb1b0_0
pyparsing                 3.0.9           py310haa95532_0
pyqt                      5.15.7          py310hd77b12b_0
pyqt5-sip                 12.11.0         py310hd77b12b_0
python                    3.10.6               hbb2ffb3_0
python-dateutil           2.8.2              pyhd3eb1b0_0
pytz                      2022.1          py310haa95532_0
pywin32                   302             py310h2bbff1b_2
pyzmq                     23.2.0          py310hd77b12b_0
qt-main                   5.15.2               he8e5bd7_7
qt-webengine              5.15.9               hb9a9bb5_4
qtwebkit                  5.212                h3ad3cdb_4
scipy                     1.9.1           py310h86744a3_0
setuptools                63.4.1          py310haa95532_0
sip                       6.6.2           py310hd77b12b_0
six                       1.16.0             pyhd3eb1b0_1
spectraplotpy             0.0.1                     dev_0    <develop>
sqlalchemy                1.4.42                   pypi_0    pypi
sqlite                    3.39.3               h2bbff1b_0
stack_data                0.2.0              pyhd3eb1b0_0
tabulate                  0.9.0                    pypi_0    pypi
texttable                 1.6.4                    pypi_0    pypi
tk                        8.6.12               h2bbff1b_0
toml                      0.10.2             pyhd3eb1b0_0
tornado                   6.2             py310h2bbff1b_0
traitlets                 5.1.1              pyhd3eb1b0_0
typing                    3.7.4.3                  pypi_0    pypi
tzdata                    2022c                h04d1e81_0
vc                        14.2                 h21ff451_1
vs2015_runtime            14.27.29016          h5e58377_2
wcwidth                   0.2.5              pyhd3eb1b0_0
wellmap                   3.4.0                    pypi_0    pypi
wheel                     0.37.1             pyhd3eb1b0_0
wincertstore              0.2             py310haa95532_2
xlrd                      2.0.1              pyhd3eb1b0_0
xlsxwriter                3.0.3                    pypi_0    pypi
xlwt                      1.3.0                    pypi_0    pypi
xz                        5.2.6                h8cc25b3_0
zeromq                    4.3.4                hd77b12b_0
zlib                      1.2.12               h8cc25b3_3
zstd                      1.5.2                h19a0ad4_0
ajasja commented 1 year ago

Great library by the way, I wish loading from excel would be combined with well-map! https://wellmap.readthedocs.io/en/latest/