Create codeql-analysis.yml (#1127)

joshmoore · web-flow · commit 363282097b14 · 2022-09-22T11:37:18.000+02:00
* Create codeql-analysis.yml see: - https://github.blog/2022-08-15-the-next-step-for-lgtm-com-github-code-scanning/ - #909 (comment) * Re-implement tempfile.mktemp using NamedTemporaryFile Adds zarr.tests.util.mktemp which can be used from all tests. The NamedTemporaryFile is immediately closed and only the path returned.
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -0,0 +1,72 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+  schedule:
+    - cron: '29 0 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+        
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines. 
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
diff --git a/zarr/tests/test_core.py b/zarr/tests/test_core.py
@@ -5,7 +5,7 @@
 import shutil
 import unittest
 from itertools import zip_longest
-from tempfile import mkdtemp, mktemp
+from tempfile import mkdtemp
 
 import numpy as np
 import pytest
@@ -53,7 +53,7 @@
     StoreV3,
 )
 from zarr.util import buffer_size
-from zarr.tests.util import abs_container, skip_test_env_var, have_fsspec
+from zarr.tests.util import abs_container, skip_test_env_var, have_fsspec, mktemp
 
 # noinspection PyMethodMayBeStatic
 
diff --git a/zarr/tests/test_creation.py b/zarr/tests/test_creation.py
@@ -1,7 +1,6 @@
 import atexit
 import os.path
 import shutil
-import tempfile
 import warnings
 
 import numpy as np
@@ -20,6 +19,7 @@
 from zarr._storage.store import v3_api_available
 from zarr._storage.v3 import DirectoryStoreV3, KVStoreV3
 from zarr.sync import ThreadSynchronizer
+from zarr.tests.util import mktemp
 
 _VERSIONS = ((None, 2, 3) if v3_api_available else (None, 2))
 _VERSIONS2 = ((2, 3) if v3_api_available else (2, ))
@@ -574,7 +574,7 @@ def test_open_like(zarr_version, at_root):
     expected_zarr_version = DEFAULT_ZARR_VERSION if zarr_version is None else zarr_version
 
     # zarr array
-    path = tempfile.mktemp()
+    path = mktemp()
     atexit.register(shutil.rmtree, path)
     z = full(100, chunks=10, dtype='f4', compressor=Zlib(5),
              fill_value=42, order='F', **kwargs)
@@ -588,7 +588,7 @@ def test_open_like(zarr_version, at_root):
     assert (z._store._store_version == z2._store._store_version ==
             expected_zarr_version)
     # numpy array
-    path = tempfile.mktemp()
+    path = mktemp()
     atexit.register(shutil.rmtree, path)
     a = np.empty(100, dtype='f4')
     z3 = open_like(a, path, chunks=10, zarr_version=zarr_version)
diff --git a/zarr/tests/test_hierarchy.py b/zarr/tests/test_hierarchy.py
@@ -32,7 +32,7 @@
                               FSStoreV3, ZipStoreV3, DBMStoreV3, LMDBStoreV3, SQLiteStoreV3,
                               LRUStoreCacheV3)
 from zarr.util import InfoReporter, buffer_size
-from zarr.tests.util import skip_test_env_var, have_fsspec, abs_container
+from zarr.tests.util import skip_test_env_var, have_fsspec, abs_container, mktemp
 
 
 _VERSIONS = ((2, 3) if v3_api_available else (2, ))
@@ -1331,7 +1331,7 @@ class TestGroupWithZipStore(TestGroup):
 
     @staticmethod
     def create_store():
-        path = tempfile.mktemp(suffix='.zip')
+        path = mktemp(suffix='.zip')
         atexit.register(os.remove, path)
         store = ZipStore(path)
         return store, None
@@ -1359,7 +1359,7 @@ class TestGroupV3WithZipStore(TestGroupWithZipStore, TestGroupV3):
 
     @staticmethod
     def create_store():
-        path = tempfile.mktemp(suffix='.zip')
+        path = mktemp(suffix='.zip')
         atexit.register(os.remove, path)
         store = ZipStoreV3(path)
         return store, None
@@ -1369,7 +1369,7 @@ class TestGroupWithDBMStore(TestGroup):
 
     @staticmethod
     def create_store():
-        path = tempfile.mktemp(suffix='.anydbm')
+        path = mktemp(suffix='.anydbm')
         atexit.register(atexit_rmglob, path + '*')
         store = DBMStore(path, flag='n')
         return store, None
@@ -1380,7 +1380,7 @@ class TestGroupV3WithDBMStore(TestGroupWithDBMStore, TestGroupV3):
 
     @staticmethod
     def create_store():
-        path = tempfile.mktemp(suffix='.anydbm')
+        path = mktemp(suffix='.anydbm')
         atexit.register(atexit_rmglob, path + '*')
         store = DBMStoreV3(path, flag='n')
         return store, None
@@ -1391,7 +1391,7 @@ class TestGroupWithDBMStoreBerkeleyDB(TestGroup):
     @staticmethod
     def create_store():
         bsddb3 = pytest.importorskip("bsddb3")
-        path = tempfile.mktemp(suffix='.dbm')
+        path = mktemp(suffix='.dbm')
         atexit.register(os.remove, path)
         store = DBMStore(path, flag='n', open=bsddb3.btopen)
         return store, None
@@ -1403,7 +1403,7 @@ class TestGroupV3WithDBMStoreBerkeleyDB(TestGroupWithDBMStoreBerkeleyDB, TestGro
     @staticmethod
     def create_store():
         bsddb3 = pytest.importorskip("bsddb3")
-        path = tempfile.mktemp(suffix='.dbm')
+        path = mktemp(suffix='.dbm')
         atexit.register(os.remove, path)
         store = DBMStoreV3(path, flag='n', open=bsddb3.btopen)
         return store, None
@@ -1414,7 +1414,7 @@ class TestGroupWithLMDBStore(TestGroup):
     @staticmethod
     def create_store():
         pytest.importorskip("lmdb")
-        path = tempfile.mktemp(suffix='.lmdb')
+        path = mktemp(suffix='.lmdb')
         atexit.register(atexit_rmtree, path)
         store = LMDBStore(path)
         return store, None
@@ -1426,7 +1426,7 @@ class TestGroupV3WithLMDBStore(TestGroupWithLMDBStore, TestGroupV3):
     @staticmethod
     def create_store():
         pytest.importorskip("lmdb")
-        path = tempfile.mktemp(suffix='.lmdb')
+        path = mktemp(suffix='.lmdb')
         atexit.register(atexit_rmtree, path)
         store = LMDBStoreV3(path)
         return store, None
@@ -1436,7 +1436,7 @@ class TestGroupWithSQLiteStore(TestGroup):
 
     def create_store(self):
         pytest.importorskip("sqlite3")
-        path = tempfile.mktemp(suffix='.db')
+        path = mktemp(suffix='.db')
         atexit.register(atexit_rmtree, path)
         store = SQLiteStore(path)
         return store, None
@@ -1447,7 +1447,7 @@ class TestGroupV3WithSQLiteStore(TestGroupWithSQLiteStore, TestGroupV3):
 
     def create_store(self):
         pytest.importorskip("sqlite3")
-        path = tempfile.mktemp(suffix='.db')
+        path = mktemp(suffix='.db')
         atexit.register(atexit_rmtree, path)
         store = SQLiteStoreV3(path)
         return store, None
diff --git a/zarr/tests/test_storage.py b/zarr/tests/test_storage.py
@@ -36,7 +36,7 @@
                           meta_root, normalize_store_arg)
 from zarr.storage import FSStore, rename, listdir
 from zarr._storage.v3 import KVStoreV3
-from zarr.tests.util import CountingDict, have_fsspec, skip_test_env_var, abs_container
+from zarr.tests.util import CountingDict, have_fsspec, skip_test_env_var, abs_container, mktemp
 from zarr.util import json_dumps
 
 
@@ -1772,7 +1772,7 @@ class TestZipStore(StoreTests):
     ZipStoreClass = ZipStore
 
     def create_store(self, **kwargs):
-        path = tempfile.mktemp(suffix='.zip')
+        path = mktemp(suffix='.zip')
         atexit.register(os.remove, path)
         store = ZipStore(path, mode='w', **kwargs)
         return store
@@ -1853,7 +1853,7 @@ def test_store_and_retrieve_ndarray(self):
 class TestDBMStore(StoreTests):
 
     def create_store(self, dimension_separator=None):
-        path = tempfile.mktemp(suffix='.anydbm')
+        path = mktemp(suffix='.anydbm')
         atexit.register(atexit_rmglob, path + '*')
         # create store using default dbm implementation
         store = DBMStore(path, flag='n', dimension_separator=dimension_separator)
@@ -1869,7 +1869,7 @@ def test_context_manager(self):
 class TestDBMStoreDumb(TestDBMStore):
 
     def create_store(self, **kwargs):
-        path = tempfile.mktemp(suffix='.dumbdbm')
+        path = mktemp(suffix='.dumbdbm')
         atexit.register(atexit_rmglob, path + '*')
 
         import dbm.dumb as dumbdbm
@@ -1881,7 +1881,7 @@ class TestDBMStoreGnu(TestDBMStore):
 
     def create_store(self, **kwargs):
         gdbm = pytest.importorskip("dbm.gnu")
-        path = tempfile.mktemp(suffix=".gdbm")  # pragma: no cover
+        path = mktemp(suffix=".gdbm")  # pragma: no cover
         atexit.register(os.remove, path)  # pragma: no cover
         store = DBMStore(
             path, flag="n", open=gdbm.open, write_lock=False, **kwargs
@@ -1893,7 +1893,7 @@ class TestDBMStoreNDBM(TestDBMStore):
 
     def create_store(self, **kwargs):
         ndbm = pytest.importorskip("dbm.ndbm")
-        path = tempfile.mktemp(suffix=".ndbm")  # pragma: no cover
+        path = mktemp(suffix=".ndbm")  # pragma: no cover
         atexit.register(atexit_rmglob, path + "*")  # pragma: no cover
         store = DBMStore(path, flag="n", open=ndbm.open, **kwargs)  # pragma: no cover
         return store  # pragma: no cover
@@ -1903,7 +1903,7 @@ class TestDBMStoreBerkeleyDB(TestDBMStore):
 
     def create_store(self, **kwargs):
         bsddb3 = pytest.importorskip("bsddb3")
-        path = tempfile.mktemp(suffix='.dbm')
+        path = mktemp(suffix='.dbm')
         atexit.register(os.remove, path)
         store = DBMStore(path, flag='n', open=bsddb3.btopen, write_lock=False, **kwargs)
         return store
@@ -1913,7 +1913,7 @@ class TestLMDBStore(StoreTests):
 
     def create_store(self, **kwargs):
         pytest.importorskip("lmdb")
-        path = tempfile.mktemp(suffix='.lmdb')
+        path = mktemp(suffix='.lmdb')
         atexit.register(atexit_rmtree, path)
         buffers = True
         store = LMDBStore(path, buffers=buffers, **kwargs)
@@ -1930,13 +1930,13 @@ class TestSQLiteStore(StoreTests):
 
     def create_store(self, **kwargs):
         pytest.importorskip("sqlite3")
-        path = tempfile.mktemp(suffix='.db')
+        path = mktemp(suffix='.db')
         atexit.register(atexit_rmtree, path)
         store = SQLiteStore(path, **kwargs)
         return store
 
     def test_underscore_in_name(self):
-        path = tempfile.mktemp(suffix='.db')
+        path = mktemp(suffix='.db')
         atexit.register(atexit_rmtree, path)
         store = SQLiteStore(path)
         store['a'] = b'aaa'
diff --git a/zarr/tests/test_storage_v3.py b/zarr/tests/test_storage_v3.py
@@ -18,7 +18,7 @@
                               LMDBStoreV3, LRUStoreCacheV3, MemoryStoreV3,
                               MongoDBStoreV3, RedisStoreV3, SQLiteStoreV3, StoreV3,
                               ZipStoreV3)
-from zarr.tests.util import CountingDictV3, have_fsspec, skip_test_env_var
+from zarr.tests.util import CountingDictV3, have_fsspec, skip_test_env_var, mktemp
 
 # pytest will fail to run if the following fixtures aren't imported here
 from .test_storage import StoreTests as _StoreTests
@@ -330,7 +330,7 @@ class TestZipStoreV3(_TestZipStore, StoreV3Tests):
     ZipStoreClass = ZipStoreV3
 
     def create_store(self, **kwargs):
-        path = tempfile.mktemp(suffix='.zip')
+        path = mktemp(suffix='.zip')
         atexit.register(os.remove, path)
         store = ZipStoreV3(path, mode='w', **kwargs)
         return store
@@ -339,7 +339,7 @@ def create_store(self, **kwargs):
 class TestDBMStoreV3(_TestDBMStore, StoreV3Tests):
 
     def create_store(self, dimension_separator=None):
-        path = tempfile.mktemp(suffix='.anydbm')
+        path = mktemp(suffix='.anydbm')
         atexit.register(atexit_rmglob, path + '*')
         # create store using default dbm implementation
         store = DBMStoreV3(path, flag='n', dimension_separator=dimension_separator)
@@ -349,7 +349,7 @@ def create_store(self, dimension_separator=None):
 class TestDBMStoreV3Dumb(_TestDBMStoreDumb, StoreV3Tests):
 
     def create_store(self, **kwargs):
-        path = tempfile.mktemp(suffix='.dumbdbm')
+        path = mktemp(suffix='.dumbdbm')
         atexit.register(atexit_rmglob, path + '*')
 
         import dbm.dumb as dumbdbm
@@ -361,7 +361,7 @@ class TestDBMStoreV3Gnu(_TestDBMStoreGnu, StoreV3Tests):
 
     def create_store(self, **kwargs):
         gdbm = pytest.importorskip("dbm.gnu")
-        path = tempfile.mktemp(suffix=".gdbm")  # pragma: no cover
+        path = mktemp(suffix=".gdbm")  # pragma: no cover
         atexit.register(os.remove, path)  # pragma: no cover
         store = DBMStoreV3(
             path, flag="n", open=gdbm.open, write_lock=False, **kwargs
@@ -373,7 +373,7 @@ class TestDBMStoreV3NDBM(_TestDBMStoreNDBM, StoreV3Tests):
 
     def create_store(self, **kwargs):
         ndbm = pytest.importorskip("dbm.ndbm")
-        path = tempfile.mktemp(suffix=".ndbm")  # pragma: no cover
+        path = mktemp(suffix=".ndbm")  # pragma: no cover
         atexit.register(atexit_rmglob, path + "*")  # pragma: no cover
         store = DBMStoreV3(path, flag="n", open=ndbm.open, **kwargs)  # pragma: no cover
         return store  # pragma: no cover
@@ -383,7 +383,7 @@ class TestDBMStoreV3BerkeleyDB(_TestDBMStoreBerkeleyDB, StoreV3Tests):
 
     def create_store(self, **kwargs):
         bsddb3 = pytest.importorskip("bsddb3")
-        path = tempfile.mktemp(suffix='.dbm')
+        path = mktemp(suffix='.dbm')
         atexit.register(os.remove, path)
         store = DBMStoreV3(path, flag='n', open=bsddb3.btopen, write_lock=False, **kwargs)
         return store
@@ -393,7 +393,7 @@ class TestLMDBStoreV3(_TestLMDBStore, StoreV3Tests):
 
     def create_store(self, **kwargs):
         pytest.importorskip("lmdb")
-        path = tempfile.mktemp(suffix='.lmdb')
+        path = mktemp(suffix='.lmdb')
         atexit.register(atexit_rmtree, path)
         buffers = True
         store = LMDBStoreV3(path, buffers=buffers, **kwargs)
@@ -404,7 +404,7 @@ class TestSQLiteStoreV3(_TestSQLiteStore, StoreV3Tests):
 
     def create_store(self, **kwargs):
         pytest.importorskip("sqlite3")
-        path = tempfile.mktemp(suffix='.db')
+        path = mktemp(suffix='.db')
         atexit.register(atexit_rmtree, path)
         store = SQLiteStoreV3(path, **kwargs)
         return store
diff --git a/zarr/tests/util.py b/zarr/tests/util.py
