From 92fbefd38bcc1527b9ddb19542b57e9625f28f48 Mon Sep 17 00:00:00 2001
From: Alexis Arnaudon <alexis.arnaudon@gmail.com>
Date: Tue, 11 Jan 2022 07:09:34 +0100
Subject: [PATCH] fix pool + add github run tox (#103)

* fix pool

* better fix

* some fix

* remove extra tqdm

* revert fast

* Apply suggestions from code review
---
 .github/workflows/run-tox.yml | 29 +++++++++++++++++++++++++++++
 .travis.yml                   |  8 --------
 hcga/extraction.py            | 27 ++++++++++-----------------
 hcga/feature_class.py         |  8 +++++++-
 4 files changed, 46 insertions(+), 26 deletions(-)
 create mode 100644 .github/workflows/run-tox.yml
 delete mode 100644 .travis.yml

diff --git a/.github/workflows/run-tox.yml b/.github/workflows/run-tox.yml
new file mode 100644
index 00000000..aee073ab
--- /dev/null
+++ b/.github/workflows/run-tox.yml
@@ -0,0 +1,29 @@
+name: Run all tox python3
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: 'true'
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip install tox-gh-actions
+    - name: Run tox
+      run: |
+        tox
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index ef8ac4c7..00000000
--- a/.travis.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-sudo: false
-language: python
-matrix:
-  include:
-    - python: 3.7
-      env: TOXENV=lint,py37
-install: pip install tox-travis
-script: tox
diff --git a/hcga/extraction.py b/hcga/extraction.py
index d7e74fd0..1ea5e809 100644
--- a/hcga/extraction.py
+++ b/hcga/extraction.py
@@ -1,7 +1,6 @@
 """Functions necessary for the extraction of graph features."""
 import logging
 import time
-from collections import defaultdict
 from functools import partial
 from importlib import import_module
 from pathlib import Path
@@ -101,18 +100,16 @@ def extract(
 
 def _print_runtimes(all_features_df):
     """Print sorted runtimes."""
-    runtimes = defaultdict(list)
-    for raw_feature in all_features_df.values():
-        for feat in raw_feature[1]:
-            runtimes[feat].append(raw_feature[1][feat])
-    feature_names, runtimes = list(runtimes.keys()), list(runtimes.values())
-    runtime_sortid = np.argsort(np.mean(runtimes, axis=1))[::-1]
-    for feat_id in runtime_sortid:
+    mean = all_features_df["runtimes"].mean(axis=0).to_list()
+    std = all_features_df["runtimes"].std(axis=0).to_list()
+    sortid = np.argsort(mean)[::-1]
+
+    for i in sortid:
         L.info(
             "Runtime of %s is %s ( std = %s ) seconds per graph.",
-            feature_names[feat_id],
-            np.round(np.mean(runtimes[feat_id]), 3),
-            np.round(np.std(runtimes[feat_id]), 3),
+            all_features_df["runtimes"].columns[i],
+            np.round(mean[i], 3),
+            np.round(std[i], 3),
         )
 
 
@@ -190,9 +187,6 @@ def feature_extraction(graph, list_feature_classes, with_runtimes=False):
     Returns:
         (DataFrame): dataframe of calculated features for a given graph.
     """
-    if with_runtimes:
-        runtimes = {}
-
     column_indexes = pd.MultiIndex(
         levels=[[], []], codes=[[], []], names=["feature_class", "feature_name"]
     )
@@ -205,14 +199,13 @@ def feature_extraction(graph, list_feature_classes, with_runtimes=False):
         features = pd.DataFrame(feat_class_inst.get_features(), index=[graph.id])
         columns = [(feat_class_inst.shortname, col) for col in features.columns]
         features_df[columns] = features
-        feat_class_inst.pool.close()
         del feat_class_inst
 
         if with_runtimes:
-            runtimes[feature_class.shortname] = time.time() - start_time
+            features_df[("runtimes", feature_class.name)] = time.time() - start_time
 
     if with_runtimes:
-        return graph.id, [features_df, runtimes]
+        return features_df
 
     return features_df
 
diff --git a/hcga/feature_class.py b/hcga/feature_class.py
index 59a24523..0eaff7a4 100644
--- a/hcga/feature_class.py
+++ b/hcga/feature_class.py
@@ -106,7 +106,7 @@ def __init__(self, graph=None):
         Args:
             graph (Graph): graph for initialisation, converted to given encoding
         """
-        self.pool = multiprocessing.Pool(processes=1)
+        self.pool = multiprocessing.Pool(processes=1, maxtasksperchild=1)
         if graph is not None:
             self.graph = graph.get_graph(self.__class__.encoding)
             self.graph_id = graph.id
@@ -115,6 +115,12 @@ def __init__(self, graph=None):
             self.graph = None
         self.features = {}
 
+    def __del__(self):
+        if hasattr(self, 'pool'):
+            self.pool.close()
+            self.pool.terminate()
+            del self.pool
+
     @classmethod
     def setup_class(
         cls,