diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
index 13deb5393..04cc9b0b5 100644
--- a/.github/workflows/ci-tests.yml
+++ b/.github/workflows/ci-tests.yml
@@ -55,7 +55,7 @@ jobs:
run: sudo usermod -c 'CI Runner' "$(whoami)"
- name: Set up Python
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
with:
python-version: ${{ env.py-semver }}
allow-prereleases: true
@@ -104,7 +104,7 @@ jobs:
fetch-depth: 0
- name: Set up Python
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
with:
python-version: ${{ env.py-semver }}
cache: pip
@@ -140,7 +140,7 @@ jobs:
run: sudo usermod -c 'CI Runner' "$(whoami)"
- name: Set up Python
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
with:
python-version: ${{ env.py-semver }}
cache: pip
@@ -194,7 +194,7 @@ jobs:
run: sudo rm -f /usr/bin/docker ; sudo apt-get install -y podman
- name: Set up Python
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
with:
python-version: 3.12
cache: pip
@@ -207,7 +207,7 @@ jobs:
CWLTOOL_OPTIONS: ${{ matrix.cwl-version == 'v1.2' && '--relax-path-checks' || '' }} ${{ matrix.extras }}
run: ./conformance-test.sh
- name: Archive test results
- uses: actions/upload-artifact@v3
+ uses: actions/upload-artifact@v4
with:
name: cwl-${{ matrix.cwl-version }}-${{ matrix.container }}${{ matrix.extras }}-conformance-results
path: |
@@ -230,7 +230,7 @@ jobs:
sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb
- name: Set up Python
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
with:
python-version: 3.12
cache: pip
@@ -272,7 +272,7 @@ jobs:
with:
fetch-depth: 0
- name: Set up Python
- uses: actions/setup-python@v4
+ uses: actions/setup-python@v5
with:
python-version: 3.12
cache: pip
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 8af9efe6f..3b84a185b 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -27,9 +27,9 @@ jobs:
# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
- uses: github/codeql-action/init@v2
+ uses: github/codeql-action/init@v3
with:
languages: python
- name: Perform CodeQL Analysis
- uses: github/codeql-action/analyze@v2
+ uses: github/codeql-action/analyze@v3
diff --git a/conformance-test.sh b/conformance-test.sh
index a1560a757..8b1e82f5b 100755
--- a/conformance-test.sh
+++ b/conformance-test.sh
@@ -76,7 +76,8 @@ else
venv "${TMP_DIR}/cwl-conformance-venv"
pip install -U setuptools wheel pip
pip uninstall -y cwltool
- pip install "${SCRIPT_DIRECTORY}" -r"${SCRIPT_DIRECTORY}/requirements.txt"
+ pip install -r"${SCRIPT_DIRECTORY}/mypy-requirements.txt"
+ CWLTOOL_USE_MYPYC=1 MYPYPATH="${SCRIPT_DIRECTORY}/mypy-stubs" pip install "${SCRIPT_DIRECTORY}" -r"${SCRIPT_DIRECTORY}/requirements.txt"
pip install 'cwltest>=2.3' pytest-cov pytest-xdist
fi
diff --git a/cwltool/command_line_tool.py b/cwltool/command_line_tool.py
index 0b0d7f3ec..5b2bea5b2 100644
--- a/cwltool/command_line_tool.py
+++ b/cwltool/command_line_tool.py
@@ -866,7 +866,7 @@ def calc_checksum(location: str) -> Optional[str]:
and "checksum" in e
and e["checksum"] != "sha1$hash"
):
- return cast(Optional[str], e["checksum"])
+ return cast(str, e["checksum"])
return None
def remove_prefix(s: str, prefix: str) -> str:
diff --git a/cwltool/process.py b/cwltool/process.py
index c442bf249..4f046928b 100644
--- a/cwltool/process.py
+++ b/cwltool/process.py
@@ -1342,10 +1342,15 @@ def compute_checksums(fs_access: StdFsAccess, fileobj: CWLObjectType) -> None:
if "checksum" not in fileobj:
checksum = hashlib.sha1() # nosec
location = cast(str, fileobj["location"])
- with fs_access.open(location, "rb") as f:
- contents = f.read(1024 * 1024)
- while contents != b"":
- checksum.update(contents)
+ if "contents" in fileobj:
+ contents = cast(str, fileobj["contents"]).encode("utf-8")
+ checksum.update(contents)
+ fileobj["size"] = len(contents)
+ else:
+ with fs_access.open(location, "rb") as f:
contents = f.read(1024 * 1024)
+ while contents != b"":
+ checksum.update(contents)
+ contents = f.read(1024 * 1024)
+ fileobj["size"] = fs_access.size(location)
fileobj["checksum"] = "sha1$%s" % checksum.hexdigest()
- fileobj["size"] = fs_access.size(location)
diff --git a/lint-requirements.txt b/lint-requirements.txt
index ef55b59e8..e33dfc2ab 100644
--- a/lint-requirements.txt
+++ b/lint-requirements.txt
@@ -1,3 +1,3 @@
flake8-bugbear<23.13
-black~=23.11
+black~=23.12
codespell
diff --git a/setup.py b/setup.py
index cc56c6889..78b4cd7e8 100644
--- a/setup.py
+++ b/setup.py
@@ -115,6 +115,7 @@
"argcomplete",
"pyparsing != 3.0.2", # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
"cwl-utils >= 0.32",
+ "spython >= 0.3.0",
],
extras_require={
"deps": [
diff --git a/tests/test_examples.py b/tests/test_examples.py
index 1e4e939c6..4d479e313 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -1325,6 +1325,28 @@ def test_cache_relative_paths(tmp_path: Path, factor: str) -> None:
assert (tmp_path / "cwltool_cache" / "27903451fc1ee10c148a0bdeb845b2cf").exists()
+@pytest.mark.parametrize("factor", test_factors)
+def test_cache_default_literal_file(tmp_path: Path, factor: str) -> None:
+ """Confirm that running a CLT with a default literal file with caching succeeds."""
+ test_file = "tests/wf/extract_region_specs.cwl"
+ cache_dir = str(tmp_path / "cwltool_cache")
+ commands = factor.split()
+ commands.extend(
+ [
+ "--out",
+ str(tmp_path / "out"),
+ "--cachedir",
+ cache_dir,
+ get_data(test_file),
+ ]
+ )
+ error_code, _, stderr = get_main_output(commands)
+
+ stderr = re.sub(r"\s\s+", " ", stderr)
+ assert "completed success" in stderr
+ assert error_code == 0
+
+
def test_write_summary(tmp_path: Path) -> None:
"""Test --write-summary."""
commands = [
diff --git a/tests/wf/extract_region_specs.cwl b/tests/wf/extract_region_specs.cwl
new file mode 100644
index 000000000..279fa4400
--- /dev/null
+++ b/tests/wf/extract_region_specs.cwl
@@ -0,0 +1,21 @@
+{
+"cwlVersion": "v1.0",
+"class": "CommandLineTool",
+"inputs": [
+ {
+ "type": "File",
+ "default": {
+ "class": "File",
+ "basename": "extract_regions.py",
+ "contents": "#!/usr/bin/env python3\n\nfrom __future__ import print_function, division\nimport sys\n\ninput_filename = sys.argv[1]\nif len(sys.argv) == 3:\n fuzz = int(sys.argv[2])\nelse:\n fuzz = 0\ninput_file = open(input_filename)\n\ncount = 0\nfor line in input_file:\n if not line.startswith(\">\"):\n continue\n count += 1\n contig_regions_file = open(\"contig_regions{}.txt\".format(count), \"w\")\n proteins_list_file = open(\"proteins{}.txt\".format(count), \"w\")\n fields = line.split(\"|\")\n protein_id = fields[0][1:]\n contig_id = fields[1]\n r_start = int(fields[6])\n if r_start > fuzz:\n r_start = r_start - fuzz\n r_end = int(fields[7]) + fuzz\n print(\"{}:{}-{}\".format(contig_id, r_start, r_end), file=contig_regions_file)\n print(protein_id, file=proteins_list_file)\n contig_regions_file.close()\n proteins_list_file.close()\n"
+ },
+ "inputBinding": {
+ "position": 1
+ },
+ "id": "scripts"
+ }
+],
+"outputs": [
+],
+"baseCommand": "cat"
+}