Small bugfix + Conda environment change for MacOS

run_tapioca.py

@@ -11,19 +11,19 @@
                       " See example input file on the Tapioca GitHub (https://github.com/FunctionLab/tapioca)"
 
 INVALID_NORM_CONTENT_MSG = "\n Error: Invalid data content/structure. %s must be reformatted to fit expected structure." \
-                      " See example normlaized input file on the Tapioca GitHub" \
-                      "(https://github.com/FunctionLab/tapioca)"
+    " See example normlaized input file on the Tapioca GitHub" \
+    "(https://github.com/FunctionLab/tapioca)"
 
 
 def validate_file(file_name, prenorm):
-    #validate file name and path.
+    # validate file name and path.
     if not valid_path(file_name):
         print(INVALID_PATH_MSG % (file_name))
         quit()
     elif not valid_filetype(file_name):
         print(INVALID_FILETYPE_MSG % (file_name))
         quit()
-    elif not validate_file_structure(file_name,prenorm):
+    elif not validate_file_structure(file_name, prenorm):
         if prenorm:
             print(INVALID_CONTENT_MSG % (file_name))
         else:
@@ -41,7 +41,8 @@ def valid_path(path):
     # validate file path
     return os.path.exists(path)
 
-def validate_file_structure(path,prenorm):
+
+def validate_file_structure(path, prenorm):
     # validate file contents
     table = pd.read_csv(path)
     cols = list(table.columns)
@@ -63,7 +64,7 @@ def validate_file_structure(path,prenorm):
             pass_flag = False
 
         for col in cols[3:]:
-            if not col.replace('.','').isnumeric():
+            if not col.replace('.', '').isnumeric():
                 print('Error: all curve data points (ex. temperatures) should be a number, '+str(col)+'is not a number.'
                       )
                 pass_flag = False
@@ -86,7 +87,8 @@ def validate_file_structure(path,prenorm):
 
 def main():
     # create parser object
-    parser = argparse.ArgumentParser(description="A Command Line Interface For Running Tapioca")
+    parser = argparse.ArgumentParser(
+        description="A Command Line Interface For Running Tapioca")
 
     # defining arguments for parser object
     parser.add_argument("-i", "--input", type=str, nargs=1,
@@ -127,24 +129,26 @@ def main():
     args.fullmodel = bool(args.fullmodel[0])
 
     # Check that the input file exists
-    if args.input == None:
+    if args.input is None:
         print('Error: No input file provided.')
         quit()
 
     # Validate the Input
     validate_file(input_check, args.prenorm)
 
-
+    # Convert Namespace object to dictionary so that
+    # if savename is not present, we can safely set a default name
+    args_dict = vars(args)  # type: Dict
 
     # If savename is None then set a default name based on the time
-    if args.savename == None:
+    if "savename" not in args_dict:
         current_datatime = str(datetime.datetime.now()).replace('-', '').replace(':', '') \
-                        .split('.')[0].replace(' ', '')
+            .split('.')[0].replace(' ', '')
         args.savename = current_datatime
     else:
         args.savename = args.savename[0]
 
-    if args.tissue == None:
+    if "tissue" not in args_dict:
         args.tissue = ''
     else:
         args.tissue = args.tissue[0]
@@ -162,4 +166,4 @@ def main():
 
 if __name__ == "__main__":
     # calling the main function
-    main()
+    main()

tapioca_env_mac.yml

@@ -1,115 +1,17 @@
 name: Tapioca
 channels:
+  - conda-forge
   - anaconda
   - defaults
 dependencies:
-  - appnope=0.1.2=py39hecd8cb5_1001
-  - argon2-cffi=21.3.0=pyhd3eb1b0_0
-  - argon2-cffi-bindings=21.2.0=py39hca72f7f_0
-  - asttokens=2.0.5=pyhd3eb1b0_0
-  - attrs=21.4.0=pyhd3eb1b0_0
-  - backcall=0.2.0=pyhd3eb1b0_0
-  - beautifulsoup4=4.11.1=py39hecd8cb5_0
-  - blas=1.0=mkl
-  - bleach=4.1.0=pyhd3eb1b0_0
-  - bottleneck=1.3.4=py39h67323c0_0
-  - ca-certificates=2022.4.26=hecd8cb5_0
-  - certifi=2022.6.15=py39hecd8cb5_0
-  - cffi=1.15.0=py39hc55c11b_1
-  - debugpy=1.5.1=py39he9d5cce_0
-  - decorator=5.1.1=pyhd3eb1b0_0
-  - defusedxml=0.7.1=pyhd3eb1b0_0
-  - entrypoints=0.4=py39hecd8cb5_0
-  - executing=0.8.3=pyhd3eb1b0_0
-  - icu=58.2=h0a44026_3
-  - intel-openmp=2021.4.0=hecd8cb5_3538
-  - ipykernel=6.9.1=py39hecd8cb5_0
-  - ipython=8.3.0=py39hecd8cb5_0
-  - ipython_genutils=0.2.0=pyhd3eb1b0_1
-  - ipywidgets=7.6.5=pyhd3eb1b0_1
-  - jedi=0.18.1=py39hecd8cb5_1
-  - jinja2=3.0.3=pyhd3eb1b0_0
-  - joblib=1.1.0=pyhd3eb1b0_0
-  - jpeg=9e=hca72f7f_0
-  - jsonschema=4.4.0=py39hecd8cb5_0
-  - jupyter=1.0.0=py39hecd8cb5_7
-  - jupyter_client=7.2.2=py39hecd8cb5_0
-  - jupyter_console=6.4.3=pyhd3eb1b0_0
-  - jupyter_core=4.10.0=py39hecd8cb5_0
-  - jupyterlab_pygments=0.1.2=py_0
-  - jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
-  - libcxx=14.0.6=h9765a3e_0
-  - libffi=3.4.2=hecd8cb5_6
-  - libgfortran=3.0.1=h93005f0_2
-  - libpng=1.6.37=ha441bb4_0
-  - libsodium=1.0.18=h1de35cc_0
-  - llvm-openmp=12.0.0=h0dcd299_1
-  - markupsafe=2.1.1=py39hca72f7f_0
-  - matplotlib-inline=0.1.2=pyhd3eb1b0_2
-  - mistune=0.8.4=py39h9ed2024_1000
-  - mkl=2021.4.0=hecd8cb5_637
-  - mkl-service=2.4.0=py39h9ed2024_0
-  - mkl_fft=1.3.1=py39h4ab4a9b_0
-  - mkl_random=1.2.2=py39hb2f4e1b_0
-  - nbclient=0.5.13=py39hecd8cb5_0
-  - nbconvert=6.4.4=py39hecd8cb5_0
-  - nbformat=5.3.0=py39hecd8cb5_0
-  - ncurses=6.4=hcec6c5f_0
-  - nest-asyncio=1.5.5=py39hecd8cb5_0
-  - notebook=6.4.11=py39hecd8cb5_0
-  - numexpr=2.8.1=py39h2e5f0a9_2
-  - numpy=1.22.3=py39h2e5f0a9_0
-  - numpy-base=1.22.3=py39h3b1a694_0
-  - openssl=1.1.1t=hca72f7f_0
-  - packaging=21.3=pyhd3eb1b0_0
-  - pandas=1.4.2=py39he9d5cce_0
-  - pandocfilters=1.5.0=pyhd3eb1b0_0
-  - parso=0.8.3=pyhd3eb1b0_0
-  - pexpect=4.8.0=pyhd3eb1b0_3
-  - pickleshare=0.7.5=pyhd3eb1b0_1003
-  - pip=23.0.1=py39hecd8cb5_0
-  - prometheus_client=0.13.1=pyhd3eb1b0_0
-  - prompt-toolkit=3.0.20=pyhd3eb1b0_0
-  - prompt_toolkit=3.0.20=hd3eb1b0_0
-  - ptyprocess=0.7.0=pyhd3eb1b0_2
-  - pure_eval=0.2.2=pyhd3eb1b0_0
-  - pycparser=2.21=pyhd3eb1b0_0
-  - pygments=2.11.2=pyhd3eb1b0_0
-  - pyparsing=3.0.4=pyhd3eb1b0_0
-  - pyqt=5.9.2=py39h23ab428_6
-  - pyrsistent=0.18.0=py39hca72f7f_0
-  - python=3.9.16=h218abb5_2
-  - python-dateutil=2.8.2=pyhd3eb1b0_0
-  - python-fastjsonschema=2.15.1=pyhd3eb1b0_0
-  - pytz=2022.1=py39hecd8cb5_0
-  - pyzmq=22.3.0=py39he9d5cce_2
-  - qt=5.9.7=h468cd18_1
-  - qtconsole=5.3.0=pyhd3eb1b0_0
-  - qtpy=2.0.1=pyhd3eb1b0_0
-  - readline=8.2=hca72f7f_0
-  - scikit-learn=0.24.2=py39hb2f4e1b_0
-  - scipy=1.7.3=py39h8c7af03_0
-  - send2trash=1.8.0=pyhd3eb1b0_1
-  - setuptools=65.6.3=py39hecd8cb5_0
-  - sip=4.19.13=py39h23ab428_0
-  - six=1.16.0=pyhd3eb1b0_1
-  - soupsieve=2.3.1=pyhd3eb1b0_0
-  - sqlite=3.41.1=h6c40b1e_0
-  - stack_data=0.2.0=pyhd3eb1b0_0
-  - terminado=0.13.1=py39hecd8cb5_0
-  - testpath=0.6.0=py39hecd8cb5_0
-  - threadpoolctl=2.2.0=pyh0d69192_0
-  - tk=8.6.12=h5d9f67b_0
-  - tornado=6.1=py39h9ed2024_0
-  - traitlets=5.1.1=pyhd3eb1b0_0
-  - typing-extensions=4.1.1=hd3eb1b0_0
-  - typing_extensions=4.1.1=pyh06a4308_0
-  - tzdata=2022g=h04d1e81_0
-  - wcwidth=0.2.5=pyhd3eb1b0_0
-  - webencodings=0.5.1=py39hecd8cb5_1
-  - wheel=0.38.4=py39hecd8cb5_0
-  - widgetsnbextension=3.5.2=py39hecd8cb5_0
-  - xz=5.2.10=h6c40b1e_1
-  - zeromq=4.3.4=h23ab428_0
-  - zlib=1.2.13=h4dc903c_0
-prefix: /opt/anaconda3/envs/Tapioca
+  - python==3.9.6
+  - jupyter==1.0.0
+  - conda-tree==1.1.0
+  - jpeg==9e
+  - sip==6.7.12
+  - scikit-learn==0.24.2
+  - typing-extensions==4.1.1
+  - icu==73.2
+  - libpng==1.6.37
+  - pandas==1.4.2
+  - libsqlite==3.45.2