* runmodels WorkingDirectory is now a named argument: --workdir (#21)

* add `--clean` option for `runmodels`
  * consequent runs can alter some models
  * check if model working directory is non empty and clean it beforehand
  * propose --clean option

Author: alexsavulescu

.github/workflows/nrn-modeldb-ci.yaml

@@ -116,7 +116,7 @@ jobs:
           python -m pip install $NEURON_V1
         fi
         nrn_ver=`python -c "from neuron import __version__ as nrn_ver; print(nrn_ver)"`
-        runmodels --virtual $nrn_ver $MODELS_TO_RUN
+        runmodels --virtual --workdir=$nrn_ver $MODELS_TO_RUN
         report2html ${nrn_ver}.json
         if [[ -d "${DROP_DIR_V1}" ]]; then
           python -m pip uninstall --yes neuron-nightly==${nrn_ver}
@@ -136,7 +136,7 @@ jobs:
           python -m pip install $NEURON_V2
         fi
         nrn_ver=`python -c "from neuron import __version__ as nrn_ver; print(nrn_ver)"`
-        runmodels --virtual $nrn_ver $MODELS_TO_RUN
+        runmodels --virtual --workdir=$nrn_ver $MODELS_TO_RUN
         report2html ${nrn_ver}.json
         if [[ -d "${DROP_DIR_V2}" ]]; then
           python -m pip uninstall --yes neuron-nightly==${nrn_ver}

README.md

@@ -25,7 +25,8 @@ The following commands are now available:
   runmodels -h
   ```
   Note that models have to be downloaded beforehand with `getmodels`.
-  You can specify `--virtual` so that NEURON GUI is run in headless mode. It requires a backend (n.r. `Xvfb`)
+  You can specify `--virtual` so that NEURON GUI is run in headless mode. It requires a backend (n.r. `Xvfb`).
+  Re-running in the same `--workdir` can mangle results. Please use `--clean` if you wish to re-run in the same `--workdir`.
 
 
 * `report2html` -> create an interactive HTML report for a given json report (obtained with `runmodels`)
@@ -103,7 +104,7 @@ The generated report following `runmodels` contains te following info:
 
 For example, by running:
 ```
-runmodels --gout test3682 3682
+runmodels --gout --workdir=test3682 3682
 ```
 we will generate report `test3782.json` :
 ```yaml

modeldb/commands.py

@@ -3,17 +3,19 @@
 from os.path import abspath
 from pprint import pprint
 from . import config
-from .modelrun import ModelRunManager
+from .modelrun import ModelRunManager, is_dir_non_empty
 from .modeldb import ModelDB
 import inspect
 import shlex
 import subprocess
 from jinja2 import Environment, FileSystemLoader
 import os
+import sys
 from .config import *
 from pathlib import Path
 from .report import diff_reports
 import json
+import shutil
 
 
 def runmodels(args=None):
@@ -22,28 +24,39 @@ def runmodels(args=None):
     Run nrn-modeldb-ci for all or specified models
 
     Usage:
-        runmodels <WorkingDirectory> [options] [<model_id>...]
+        runmodels --workdir=<PATH> [options] [<model_id>...]
         runmodels -h    Print help
 
     Arguments:
-        WorkingDirectory=PATH   Required: directory where to run the models and store the reports
+        --workdir=<PATH>          Required: directory where to run the models and store the reports
         model_id=<n>            Optional: ModelDB accession number(s) to run; default is all available models
 
     Options:
         --gout                  Include gout into the report. Note that gout data can be very big, so disabled by default.
         --virtual               Run in headless mode. You need a back-end like Xvfb.
+        --clean                 Auto-clean model working directory before running (useful for consecutive runs and failsafe)
 
     Examples
-        runmodels /path/to/workdir
-        runmodels /path/to/workdir 23613 12344
+        runmodels --workdir=/path/to/workdir                        # run all models
+        runmodels --clean --workdir=/path/to/workdir 23613 12344    # run models 23613 & 12344
     """
     options = docopt(runmodels.__doc__, args)
-    working_dir = options.pop("<WorkingDirectory>")
+    working_dir = options.pop("--workdir")
     model_ids = [int(model_id) for model_id in options.pop("<model_id>")]
     gout = options.pop("--gout", False)
     virtual = options.pop("--virtual", False)
+    clean = options.pop("--clean", False)
 
-    mrm = ModelRunManager(working_dir, gout=gout)
+    if os.path.abspath(working_dir) == ROOT_DIR:
+        print("Cannot run models directly into nrn-modeldb-ci ROOT_DIR -> {}".format(ROOT_DIR))
+        sys.exit(1)
+
+    if not clean and is_dir_non_empty(working_dir):
+        print("WARNING: WorkingDirectory {} exists and is non empty.".format(working_dir))
+        print("\tre-run with --clean if you wish to overwrite model runs!")
+        sys.exit(1)
+
+    mrm = ModelRunManager(working_dir, gout=gout, clean=clean)
     model_list = model_ids if model_ids else None
 
     if virtual:
@@ -102,7 +115,7 @@ def diffgout(args=None):
     cmd = 'nrngui -c "strdef gout1" -c "gout1=\\"{}\\"" -c "strdef gout2" -c "gout2=\\"{}\\"" modeldb/showgout.hoc'.format(
         gout_file1, gout_file2)
     commands = shlex.split(cmd)
-    p = subprocess.Popen(commands)
+    _ = subprocess.Popen(commands)
 
 
 def modeldb_config(args=None):
@@ -204,4 +217,4 @@ def diffreports2html(args=None):
             diff_dict=diff_dict,
             gout_dict=gout_dict),
         )
-    print('Done.')
+    print('Done.')

modeldb/modelrun.py

@@ -13,11 +13,26 @@
 import traceback
 import json
 import time
+import shutil
 
 ModelDB = modeldb.ModelDB()
 
+
+def is_dir_non_empty(directory):
+    """
+    Returns True if the `directory` exists and is non-empty
+    """
+    try:
+        if any(os.scandir(directory)):
+            return True
+    except Exception:  # noqa
+        pass
+
+    return False
+
+
 class ModelRun(dict):
-    def __init__(self, model, working_dir):
+    def __init__(self, model, working_dir, clean=False):
         self._model = model
         self._working_dir = os.path.abspath(working_dir)
         self._logs = []
@@ -27,6 +42,7 @@ def __init__(self, model, working_dir):
         self._no_mosinit_hoc = False
         self._run_time = 0
         self._run_py = False
+        self._clean = clean
 
         self["run_info"] = {}
 
@@ -161,10 +177,13 @@ def prepare_model(model):
     with zipfile.ZipFile(
             os.path.join(MODELS_ZIP_DIR, str(model.id) + ".zip"), "r"
     ) as zip_ref:
-        zip_ref.extractall(model.working_dir)
-        model.run_info["model_dir"] = os.path.join(
+        model_dir = os.path.join(
             model.working_dir, os.path.dirname(zip_ref.infolist()[0].filename)
         )
+        if model._clean and is_dir_non_empty(model_dir):
+            shutil.rmtree(model_dir)
+        zip_ref.extractall(model.working_dir)
+        model.run_info["model_dir"] = model_dir
 
     # write driver.hoc
     build_driver_hoc(model)
@@ -249,7 +268,7 @@ def run_model(model):
 
 
 class ModelRunManager(object):
-    def __init__(self, master_dir, gout=False):
+    def __init__(self, master_dir, gout=False, clean=False):
         self.master_dir = master_dir
         self.logfile = str(master_dir) + ".log"
         self.dumpfile = str(master_dir) + ".json"
@@ -259,6 +278,7 @@ def __init__(self, master_dir, gout=False):
         )
         self.run_logs = {}
         self._gout = gout
+        self._clean = clean
 
     def _setup_logging(self):
         self.logger = logging.getLogger("dev")
@@ -380,7 +400,7 @@ def run_models(self, model_list=None):
 
         # prepare ModelRun objects
         models_to_run = (
-            ModelRun(mdl, self.master_dir) for mdl in models_selected
+            ModelRun(mdl, self.master_dir, self._clean) for mdl in models_selected
         )
 
         # number of models