Merge pull request #4 from haniffalab/hist

Added history command

bin/cmdbase/__init__.py

@@ -1,2 +1,2 @@
-from . import alignment, irods, rna
+from . import alignment, irods, rna, basic
 from .helpers import *

bin/cmdbase/basic/__init__.py

@@ -0,0 +1 @@
+from .history import *

bin/cmdbase/basic/history.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python3
+
+import click
+import os
+from tabulate import tabulate
+import pandas as pd
+
+@click.command("history")
+
+@click.option("--last", required=False,  help="Retrieve last n commands",
+              default=10, type = int)
+
+@click.option(
+    "--all",
+    default=False,
+    is_flag=True,
+    required=False,
+    help="Retrieve all history",
+)
+
+def history(last, all):
+    CWD = os.environ['CWD']
+    hist_file = os.path.join(CWD, ".pap/") + "hist"
+    if not os.path.exists(hist_file):
+        click.echo("No history file present")
+        return 0
+    hist = pd.read_csv(hist_file, index_col = 0)
+    if all:
+        print(tabulate(hist, headers='keys', tablefmt='plain'))
+    else:
+        print(tabulate(hist.tail(last), headers='keys', tablefmt='plain'))
+    return 0

bin/cmdbase/basic/test.py

@@ -0,0 +1,9 @@
+#!/usr/bin/env python3
+
+import click
+
+
+@click.command("test_import")
+def test_import1():
+    print("Hello World")
+    return 0

bin/hl..piperv100

@@ -40,6 +40,7 @@ os.environ["GLOBAL_HIST"] = GLOBAL_HIST
 os.environ["LOCAL_HIST"] = LOCAL_HIST
 os.environ["VERSION"] = VERSION
 os.environ["RUN_TOKEN"] = RUN_TOKEN
+os.environ["CWD"] = CWD
 #### Create options that can common to all ####
 
 
@@ -115,15 +116,18 @@ def argtest(user_params, **kwargs):
 
 ####
 
+################# basic commands ###########
+cli.add_command(cmdbase.basic.history)
+
 
 ################ irods commands ################
 irods.add_command(cmdbase.irods.pull_processed)
 irods.add_command(cmdbase.irods.pull_fastqs)
 
-################### scrna seq analysis commands ###################
+################# scrna seq analysis commands ##
 rna.add_command(cmdbase.rna.cellbender)
 
-################# alignment commands ###################
+################# alignment commands ###########
 alignment.add_command(cmdbase.alignment.cellranger)
 alignment.add_command(cmdbase.alignment.starsolo)