Fix codecov

.circleci/config.yml

@@ -1,4 +1,8 @@
-version: 2
+version: 2.1
+
+orbs:
+  codecov: codecov/[email protected]
+
 jobs:
   build:
     docker:
@@ -27,9 +31,11 @@ jobs:
             # Run setup.py so that the version is defined
             python3 setup.py build
             python3 -m pytest --cov=tszip --cov-report=xml --cov-branch -n 2 tests
-            codecov
             rm .coverage
 
+      - codecov/upload:
+          token: CODECOV_TOKEN
+
       - run:
           name: Build Python package
           command: |

.github/workflows/tests.yml

@@ -8,22 +8,22 @@ on:
 jobs:
   pre-commit:
     name: Lint
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
         uses: styfle/[email protected]
         with:
           access_token: ${{ github.token }}
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: pre-commit/action@v2.0.0
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+      - uses: pre-commit/action@v3.0.0
 
   test:
     name: Python
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.7, 3.9 ]
+        python: [ 3.8, "3.10" ]
         os:  [ macos-latest, ubuntu-latest, windows-latest ]
     defaults:
       run:
@@ -48,7 +48,7 @@ jobs:
             /usr/share/miniconda/envs/anaconda-client-env
             ~/osx-conda
             ~/.profile
-          key: ${{ runner.os }}-${{ matrix.python}}-conda-v10-${{ hashFiles('requirements/CI-tests-conda.txt') }}
+          key: ${{ runner.os }}-${{ matrix.python}}-conda-v12-${{ hashFiles('requirements/CI-tests-conda.txt') }}
 
       - name: Install Conda
         uses: conda-incubator/setup-miniconda@v2

.mergify.yml

@@ -31,7 +31,6 @@ pull_request_rules:
       queue:
         name: default
         method: rebase
-        rebase_fallback: none
         update_method: rebase
 
   - name: Remove label after merge

.pre-commit-config.yaml

@@ -1,28 +1,28 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.4.0
     hooks:
       - id: check-merge-conflict
       - id: debug-statements
       - id: mixed-line-ending
       - id: check-case-conflict
       - id: check-yaml
   - repo: https://github.com/asottile/reorder_python_imports
-    rev: v2.4.0
+    rev: v3.9.0
     hooks:
       - id: reorder-python-imports
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.12.0
+    rev: v3.3.1
     hooks:
       - id: pyupgrade
         args: [--py3-plus, --py36-plus]
   - repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 23.3.0
     hooks:
       - id: black
         language_version: python3
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.9.1
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
     hooks:
       - id: flake8
         args: [--config=.flake8]

requirements/CI-tests-conda.txt

@@ -4,5 +4,5 @@ msprime==1.1.0
 pytest==6.2.5
 pytest-cov==3.0.0
 pytest-xdist==2.5.0
-tskit==0.4.1
+tskit==0.5.4
 zarr==2.10.3

requirements/development.txt

@@ -1,4 +1,3 @@
-codecov
 coverage
 flake8
 h5py

tests/test_cli.py

@@ -288,11 +288,10 @@ def test_bad_file_format(self):
             with self.assertRaises(TestException):
                 self.run_tszip([str(self.trees_path)])
             mocked_exit.assert_called_once_with(
-                f"Error loading '{self.trees_path}': File not in kastore format. If this"
-                f" file was generated by msprime < 0.6.0 (June 2018) it uses the old"
-                f" HDF5-based format which can no longer be read directly. Please"
-                f" convert to the new kastore format using the ``tskit upgrade``"
-                f" command."
+                f"Error loading '{self.trees_path}': File not in kastore format. Either"
+                f" the file is corrupt or it is not a tskit tree sequence file. It may"
+                f" be a legacy HDF file upgradable with `tskit upgrade` or a compressed"
+                f" tree sequence file that can be decompressed with `tszip`."
             )
 
     def test_compress_stdout_keep(self):

tests/test_compression.py

@@ -57,36 +57,36 @@ def test_int16(self):
         self.verify(
             np.int16,
             np.array(
-                [2 ** 15 - 1, -(2 ** 15) + 1, 2 ** 7 + 1, -(2 ** 7) - 1], dtype=np.int64
+                [2**15 - 1, -(2**15) + 1, 2**7 + 1, -(2**7) - 1], dtype=np.int64
             ),
         )
 
     def test_uint16(self):
-        self.verify(np.uint16, np.array([256, 2 ** 16 - 1], dtype=np.uint64))
+        self.verify(np.uint16, np.array([256, 2**16 - 1], dtype=np.uint64))
 
     def test_int32(self):
         self.verify(
             np.int32,
             np.array(
-                [2 ** 31 - 1, -(2 ** 31) + 1, 2 ** 15 + 1, -(2 ** 15) - 1],
+                [2**31 - 1, -(2**31) + 1, 2**15 + 1, -(2**15) - 1],
                 dtype=np.int64,
             ),
         )
 
     def test_uint32(self):
-        self.verify(np.uint32, np.array([2 ** 16 + 1, 2 ** 32 - 1], dtype=np.uint64))
+        self.verify(np.uint32, np.array([2**16 + 1, 2**32 - 1], dtype=np.uint64))
 
     def test_int64(self):
         self.verify(
             np.int64,
             np.array(
-                [2 ** 63 - 1, -(2 ** 63) + 1, 2 ** 31 + 1, -(2 ** 31) - 1],
+                [2**63 - 1, -(2**63) + 1, 2**31 + 1, -(2**31) - 1],
                 dtype=np.int64,
             ),
         )
 
     def test_uint64(self):
-        self.verify(np.uint64, np.array([2 ** 32 + 1, 2 ** 64 - 1], dtype=np.uint64))
+        self.verify(np.uint64, np.array([2**32 + 1, 2**64 - 1], dtype=np.uint64))
 
     def test_float32(self):
         self.verify(np.float32, np.array([0.1, 1e-3], dtype=np.float32))

tszip/compression.py

@@ -107,7 +107,7 @@ def compress(ts, destination, variants_only=False):
         else:
             # Assume that destination is a file-like object open in "wb" mode.
             with open(filename, "rb") as source:
-                chunk_size = 2 ** 10  # 1MiB
+                chunk_size = 2**10  # 1MiB
                 for chunk in iter(functools.partial(source.read, chunk_size), b""):
                     destination.write(chunk)
 
@@ -167,7 +167,6 @@ def compress(self, root, compressor):
 
 
 def compress_zarr(ts, root, variants_only=False):
-
     provenance_dict = provenance.get_provenance_dict({"variants_only": variants_only})
 
     if variants_only: