more changes to integration test

requirements.txt

@@ -30,3 +30,4 @@ isort==5.8.0
 flake8==3.9.2
 black==21.5b1
 pre-commit==2.12.1
+pytest-order==0.11.0

umami/tests/integration/fixtures/testSetup.yaml

@@ -19,8 +19,8 @@ test_umami:
     preprocessing_config: 'examples/PFlow-Preprocessing.yaml'
     plotting_config: 'examples/plotting_umami_config_Umami.yaml'
     testdir: '/tmp/umami/umami'
-    files:
-        - PFlow-hybrid_70-test-preprocessed_shuffled.h5
-        - PFlow-scale_dict.json
-        - MC16d_hybrid_odd_100_PFlow-no_pTcuts-file_0.h5
-        - MC16d_hybrid-ext_odd_0_PFlow-no_pTcuts-file_0.h5
+    # files:
+    #     - PFlow-hybrid_70-test-preprocessed_shuffled.h5
+    #     - PFlow-scale_dict.json
+    #     - MC16d_hybrid_odd_100_PFlow-no_pTcuts-file_0.h5
+    #     - MC16d_hybrid-ext_odd_0_PFlow-no_pTcuts-file_0.h5

umami/tests/integration/test_preprocessing.py

 import logging
 import os
 import unittest
+
 from subprocess import CalledProcessError, run
 
 import yaml
@@ -112,11 +113,17 @@ class TestPreprocessing(unittest.TestCase):
         self.data = getConfiguration()
 
         test_dir = os.path.join(self.data["test_preprocessing"]["testdir"])
+        test_dir_dl1r = os.path.join(self.data["test_preprocessing"]["testdir"])
+        test_dir_dips = os.path.join(self.data["test_preprocessing"]["testdir"])
+        test_dir_umami = os.path.join(self.data["test_preprocessing"]["testdir"])
         logging.info(f"Creating test directory in {test_dir}")
         # clean up, hopefully this causes no "uh oh...""
         if test_dir.startswith("/tmp"):
             run(["rm", "-rf", test_dir])
         run(["mkdir", "-p", test_dir])
+        run(["mkdir", "-p", test_dir_dl1r])
+        run(["mkdir", "-p", test_dir_dips])
+        run(["mkdir", "-p", test_dir_umami])
 
         # inputs for test will be located in test_dir
         config_source = os.path.join(
@@ -135,14 +142,20 @@ class TestPreprocessing(unittest.TestCase):
         self.var_dict_dl1r = os.path.join(
             test_dir, os.path.basename(var_dict_dl1r_source)
         )
+        self.scale_dict_dl1r = os.path.join(test_dir_dl1r, "PFlow-scale_dict.json")
+        self.output_dl1r = os.path.join(test_dir_dl1r, "PFlow-hybrid_70-test.h5")
+
         self.var_dict_dips = os.path.join(
             test_dir, os.path.basename(var_dict_dips_source)
         )
+        self.scale_dict_dips = os.path.join(test_dir_dips, "PFlow-scale_dict.json")
+        self.output_dips = os.path.join(test_dir_dips, "PFlow-hybrid_70-test.h5")
+
         self.var_dict_umami = os.path.join(
             test_dir, os.path.basename(var_dict_umami_source)
         )
-        self.scale_dict = os.path.join(test_dir, "PFlow-scale_dict.json")
-        self.output = os.path.join(test_dir, "PFlow-hybrid_70-test.h5")
+        self.scale_dict_umami = os.path.join(test_dir_umami, "PFlow-scale_dict.json")
+        self.output_umami = os.path.join(test_dir_umami, "PFlow-hybrid_70-test.h5")
 
         logging.info(
             f"Preparing config file based on {config_source} in {self.config}..."

umami/tests/integration/test_train_umami.py

 import logging
 import os
 import unittest
+import pytest
 from subprocess import CalledProcessError, run
 import yaml
-from umami.tools import replaceLineInFile, replaceFirstLineInFile, yaml_loader
+from umami.tools import replaceLineInFile, yaml_loader
 
 
 def getConfiguration():
@@ -153,30 +154,33 @@ class TestUmami(unittest.TestCase):
             self.config, "var_dict:", f"var_dict: {self.var_dict_umami}"
         )
         replaceLineInFile(self.config, "batch_size:", "    batch_size: 10")
-        replaceFirstLineInFile(
-            self.config, "train_file:", f"train_file: {self.train_file}"
+        replaceLineInFile(
+            self.config, "train_file:", f"train_file: {self.train_file}", onlyFirstOccurence=True
         )
-        replaceFirstLineInFile(
-            self.config, "validation_file:", f"validation_file: {self.test_file_ttbar}"
+        replaceLineInFile(
+            self.config, "validation_file:", f"validation_file: {self.test_file_ttbar}", onlyFirstOccurence=True
         )
-        replaceFirstLineInFile(
-            self.config, "add_validation_file:", f"add_validation_file: {self.test_file_zprime}"
+        replaceLineInFile(
+            self.config, "add_validation_file:", f"add_validation_file: {self.test_file_zprime}", onlyFirstOccurence=True
         )
-        replaceFirstLineInFile(
-            self.config, "test_file:", f"test_file: {self.test_file_ttbar}"
+        replaceLineInFile(
+            self.config, "test_file:", f"test_file: {self.test_file_ttbar}", onlyFirstOccurence=True
         )
-        replaceFirstLineInFile(
-            self.config, "add_test_file:", f"add_test_file: {self.test_file_zprime}"
+        replaceLineInFile(
+            self.config, "add_test_file:", f"add_test_file: {self.test_file_zprime}", onlyFirstOccurence=True
         )
         # evaluation parameters
-        replaceFirstLineInFile(
-            self.config, "n_jets:", "    n_jets: 2500"
+        replaceLineInFile(
+            self.config, "n_jets:", "    n_jets: 2500", onlyFirstOccurence=True
         )
-        replaceFirstLineInFile(
-            self.config, "fc_value:", "    fc_value: 0.018"
+        replaceLineInFile(
+            self.config, "fc_value:", "    fc_value: 0.018", onlyFirstOccurence=True
         )
-        replaceFirstLineInFile(
-            self.config, "WP_b:", "    WP_b: 0.77"
+        replaceLineInFile(
+            self.config, "WP_b:", "    WP_b: 0.77", onlyFirstOccurence=True
+        )
+        replaceLineInFile(
+            self.config, "Path:", f"        Path: {self.test_file_ttbar}"
         )
 
         logging.info("Downloading test data...")
@@ -189,6 +193,7 @@ class TestUmami(unittest.TestCase):
             logging.info(f"Retrieving file from path {path}")
             run(["wget", path, "--directory-prefix", test_dir])
 
+    @pytest.mark.order(after="test_preprocessing_umami")
     def test_umami(self):
         """Integration test of train_umami.py script."""
         self.assertTrue(

umami/tools/__init__.py

 # flake8: noqa
 from umami.tools.PyATLASstyle.PyATLASstyle import applyATLASstyle, makeATLAStag
-from umami.tools.tools import replaceLineInFile, replaceFirstLineInFile, yaml_loader
+from umami.tools.tools import replaceLineInFile, yaml_loader

umami/tools/tools.py

@@ -21,24 +21,12 @@ yaml_loader.add_implicit_resolver(
 )
 
 
-def replaceLineInFile(file, key, newLine):
-    filedata = ""
-    with open(file, "r") as f:
-        for line in f:
-            if key in line:
-                line = newLine + "\n"
-            filedata += line
-
-    with open(file, "w") as f:
-        f.write(filedata)
-
-
-def replaceFirstLineInFile(file, key, newLine):
+def replaceLineInFile(file, key, newLine, onlyFirstOccurence=False):
     filedata = ""
     replacedLine = False
     with open(file, "r") as f:
         for line in f:
-            if key in line and not replacedLine:
+            if key in line and not (onlyFirstOccurence and replacedLine):
                 line = newLine + "\n"
                 replacedLine = True
             filedata += line