Fixing deployment reliability issues and fixing documentation

.devcontainer/Dockerfile

@@ -14,13 +14,6 @@ RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
     && apt-get -y install --no-install-recommends git-flow \
     && apt-get -y install --no-install-recommends cmake
 
-# Setup R
-RUN apt update \
-    && apt install -y dirmngr gnupg apt-transport-https ca-certificates software-properties-common \
-    && apt install r-base -y 
-
-RUN chown -R vscode:vscode /usr/local/lib/R/site-library
-
 # [Optional] If your pip requirements rarely change, uncomment this section to add them to the image.
  COPY docs/dev_requirements.txt /tmp/pip-tmp/
  RUN pip3 --disable-pip-version-check --no-cache-dir install -r /tmp/pip-tmp/dev_requirements.txt \

.devcontainer/devcontainer.json

@@ -7,7 +7,7 @@
 		"context": "..",
 		"args": { 
 			"PROJECT_NAME": "HRV in MEG",
-            "PYTHON": "3.8.3",
+            "PYTHON": "3.10",
             "USERNAME": "vscode",
 			"NODE_VERSION": "none"
 		}
@@ -62,8 +62,5 @@
 				
 
 	// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
-	"remoteUser": "vscode",
-	"features": {
-		"git": "latest"
-	}
+	"remoteUser": "vscode"
 }
\ No newline at end of file

config/args_meg_preproc.json

@@ -6,5 +6,5 @@
     "bandpass_highfreq_cutoff": 100,
     "sampling_freq": 1200,
     "downsample_freq":500,
-    "intermediate_filename":"heartifact.csv"
+    "intermediate_filename":"heartifacttest.csv"
 }
\ No newline at end of file

config/run_id.txt

-74e293646401442f8854f00fc9027fd9
\ No newline at end of file

hrv_meg/main.py

@@ -78,17 +78,17 @@ def preprocess_megs(
                 mlflow.log_params(args)
                 mlflow.log_param("output_filepath", full_csv_output_path)
 
-        # Save to config folder
-        open(Path(config.CONFIG_DIR, "run_id.txt"), "w", encoding="utf-8").write(run_id)
-        if counter < len(meg_scan_folders):
-            counter = counter + 1
-            print("counter - ", counter)
-        else:
-            output_filepath = Path(config.INTERMEDIATE_DIR, "output_ica_files.txt")
-            with open(output_filepath, "w", encoding="utf-8") as f:
-                for item in output_files:
-                    str_item = str(item)
-                    f.write("%s,\n" % str_item)
+            # Save to config folder
+            open(Path(config.CONFIG_DIR, "run_id.txt"), "w", encoding="utf-8").write(run_id)
+            if counter < len(meg_scan_folders):
+                counter = counter + 1
+                print("counter - ", counter)
+            else:
+                output_filepath = Path(config.INTERMEDIATE_DIR, "output_ica_files.txt")
+                with open(output_filepath, "w", encoding="utf-8") as f:
+                    for item in output_files:
+                        str_item = str(item)
+                        f.write("%s,\n" % str_item)
 
 
 @app.command()

hrv_meg/preprocess_ecg.py

@@ -2,7 +2,7 @@ from pathlib import Path
 
 import neurokit2 as nk
 import pandas as pd
-import plotter
+from hrv_meg import plotter
 
 
 def nk_preproc(ecg_signal, fs):