Merge pull request #84 from inab/jmfernandez

Reimplemented the export machinery and version bump to 0.10.0

.pytest.ini

@@ -1,2 +1,5 @@
 [pytest]
+pythonpath = .
 testpaths = tests
+required_plugins = pytest_param_files
+addopts = --order-dependencies

CITATION.cff

@@ -15,7 +15,7 @@ authors:
     given-names: Daniel
     orcid: "https://orcid.org/0000-0001-8152-0398"
 cff-version: 1.2.0
-date-released: "2023-11-07"
+date-released: "2024-04-24"
 identifiers:
   - description: WfExS-backend release in Zenodo
     type: doi
@@ -28,4 +28,4 @@ message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/inab/WfExS-backend"
 type: software
 title: "WfExS-backend"
-version: 0.10.2
+version: 0.99.0

INSTALL.md

@@ -128,7 +128,13 @@ As these checks are applied only to the python version currently being used in t
 there is a GitHub workflow at [.github/workflows/pre-commit.yml](.github/workflows/pre-commit.yml)
 which runs them on several Python versions.
 
-If you have lots of cores, fast disks and docker installed, you can locally run the pre-commit GitHub workflow using [act](https://github.com/nektos/act):
+Although there are few tests covering the code, they can be tried using next command line:
+
+```bash
+pytest
+```
+
+Last, if you have lots of cores, fast disks and docker installed, you can locally run the pre-commit GitHub workflow using [act](https://github.com/nektos/act):
 
 ```bash
 act -j pre-commit

TODO.md

@@ -45,13 +45,15 @@ references to the inputs, that we are going to use to instantiate the workflows.
 
   - [ ] **Step 7.f**: Upload workflow to WorkflowHub.
 
-  - [ ] **Step 7.g**: Upload to Zenodo.
+  - [x] **Step 7.g**: Upload to Zenodo.
 
-  - [ ] **Step 7.h**: Upload to B2SHARE.
+  - [x] **Step 7.h**: Upload to B2SHARE.
 
   - [ ] **Step 7.i**: Upload to osf.io .
 
   - [ ] **Setp 7.j**: Explore datacite doi service.
+
+  - [x] **Step 7.k**: Upload to Dataverse.
 
 - [ ] **Step 8**: (partially implemented) Create execution provenance, which includes uploading URLs of results and / or DOIs / URIs.
 

dev-requirements.txt

@@ -3,6 +3,10 @@ pylint < 2.14.0 ; python_version == '3.6'
 pylint >= 2.15.5 ; python_version >= '3.7'
 pytest
 pytest-cov
+pytest-dependency @ git+https://github.com/jmfernandez/[email protected]
+pytest-env
+pytest-order
+pytest_param_files
 pytest-xdist
 pyflakes >= 2.5.0
 flake8 < 6.0.0 ; python_version < '3.8'

mypy-requirements.txt

@@ -7,6 +7,8 @@ types-jsonschema
 types-mypy-extensions
 types-openpyxl
 types-paramiko
+types-pluggy
+types-pyxdg
 types-PyYAML
 types-requests
 types-setuptools

mypy-stubs/defusedxml/ElementTree.pyi

@@ -0,0 +1,100 @@
+from collections.abc import Iterator, Sequence
+from typing import Any
+from _typeshed import SupportsRead
+from xml.etree.ElementTree import (
+    Element,
+    ElementTree,
+    ParseError as ParseError,
+    TreeBuilder as _TreeBuilder,
+    XMLParser as _XMLParser,
+    tostring as tostring,
+)
+
+class DefusedXMLParser(_XMLParser):
+    forbid_dtd: bool
+    forbid_entities: bool
+    forbid_external: bool
+    def __init__(
+        self,
+        html: object | bool = ...,
+        target: _TreeBuilder | None = None,
+        encoding: str | None = None,
+        forbid_dtd: bool = False,
+        forbid_entities: bool = True,
+        forbid_external: bool = True,
+    ) -> None: ...
+    def defused_start_doctype_decl(
+        self,
+        name: str | None,
+        sysid: str | None,
+        pubid: str | None,
+        has_internal_subset: bool,
+    ) -> None: ...
+    def defused_entity_decl(
+        self,
+        name: str | None,
+        is_parameter_entity: bool,
+        value: str | None,
+        base: str | None,
+        sysid: str | None,
+        pubid: str | None,
+        notation_name: str | None,
+    ) -> None: ...
+    def defused_unparsed_entity_decl(
+        self,
+        name: str | None,
+        base: str | None,
+        sysid: str | None,
+        pubid: str | None,
+        notation_name: str | None,
+    ) -> None: ...
+    def defused_external_entity_ref_handler(
+        self,
+        context: str | None,
+        base: str | None,
+        sysid: str | None,
+        pubid: str | None,
+    ) -> None: ...
+
+XMLTreeBuilder = DefusedXMLParser
+XMLParse = DefusedXMLParser
+XMLParser = DefusedXMLParser
+
+# wrapper to xml.etree.ElementTree.parse
+def parse(
+    source: str | SupportsRead[bytes] | SupportsRead[str],
+    parser: _XMLParser | None = None,
+    forbid_dtd: bool = False,
+    forbid_entities: bool = True,
+    forbid_external: bool = True,
+) -> ElementTree: ...
+
+# wrapper to xml.etree.ElementTree.iterparse
+def iterparse(
+    source: str | SupportsRead[bytes] | SupportsRead[str],
+    events: Sequence[str] | None = None,
+    parser: _XMLParser | None = None,
+    forbid_dtd: bool = False,
+    forbid_entities: bool = True,
+    forbid_external: bool = True,
+) -> Iterator[tuple[str, Any]]: ...
+def fromstring(
+    text: str,
+    forbid_dtd: bool = False,
+    forbid_entities: bool = True,
+    forbid_external: bool = True,
+) -> Element: ...
+
+XML = fromstring
+
+__all__ = [
+    "ParseError",
+    "XML",
+    "XMLParse",
+    "XMLParser",
+    "XMLTreeBuilder",
+    "fromstring",
+    "iterparse",
+    "parse",
+    "tostring",
+]

mypy-stubs/defusedxml/METADATA.toml

@@ -0,0 +1,7 @@
+version = "0.7.*"
+upstream_repository = "https://github.com/tiran/defusedxml"
+partial_stub = true
+
+[tool.stubtest]
+ignore_missing_stub = true
+stubtest_requirements = ["lxml"]

mypy-stubs/defusedxml/__init__.pyi

@@ -0,0 +1,15 @@
+from .common import (
+    DefusedXmlException as DefusedXmlException,
+    DTDForbidden as DTDForbidden,
+    EntitiesForbidden as EntitiesForbidden,
+    ExternalReferenceForbidden as ExternalReferenceForbidden,
+    NotSupportedError as NotSupportedError,
+)
+
+__all__ = [
+    "DefusedXmlException",
+    "DTDForbidden",
+    "EntitiesForbidden",
+    "ExternalReferenceForbidden",
+    "NotSupportedError",
+]

mypy-stubs/defusedxml/cElementTree.pyi

@@ -0,0 +1,23 @@
+from .ElementTree import (
+    XML as XML,
+    ParseError as ParseError,
+    XMLParse as XMLParse,
+    XMLParser as XMLParser,
+    XMLTreeBuilder as XMLTreeBuilder,
+    fromstring as fromstring,
+    iterparse as iterparse,
+    parse as parse,
+    tostring as tostring,
+)
+
+__all__ = [
+    "ParseError",
+    "XML",
+    "XMLParse",
+    "XMLParser",
+    "XMLTreeBuilder",
+    "fromstring",
+    "iterparse",
+    "parse",
+    "tostring",
+]

mypy-stubs/defusedxml/common.pyi

@@ -0,0 +1,43 @@
+PY3: bool
+
+class DefusedXmlException(ValueError): ...
+
+class DTDForbidden(DefusedXmlException):
+    name: str | None
+    sysid: str | None
+    pubid: str | None
+    def __init__(
+        self, name: str | None, sysid: str | None, pubid: str | None
+    ) -> None: ...
+
+class EntitiesForbidden(DefusedXmlException):
+    name: str | None
+    value: str | None
+    base: str | None
+    sysid: str | None
+    pubid: str | None
+    notation_name: str | None
+    def __init__(
+        self,
+        name: str | None,
+        value: str | None,
+        base: str | None,
+        sysid: str | None,
+        pubid: str | None,
+        notation_name: str | None,
+    ) -> None: ...
+
+class ExternalReferenceForbidden(DefusedXmlException):
+    context: str | None
+    base: str | None
+    sysid: str | None
+    pubid: str | None
+    def __init__(
+        self,
+        context: str | None,
+        base: str | None,
+        sysid: str | None,
+        pubid: str | None,
+    ) -> None: ...
+
+class NotSupportedError(DefusedXmlException): ...

mypy-stubs/defusedxml/expatbuilder.pyi

@@ -0,0 +1,53 @@
+from _typeshed import SupportsRead
+from xml.dom.expatbuilder import (
+    ExpatBuilder as _ExpatBuilder,
+    Namespaces as _Namespaces,
+)
+from xml.dom.minidom import Document
+from xml.dom.xmlbuilder import Options
+
+__origin__: str
+
+class DefusedExpatBuilder(_ExpatBuilder):
+    forbid_dtd: bool
+    forbid_entities: bool
+    forbid_external: bool
+    def __init__(
+        self,
+        options: Options | None = None,
+        forbid_dtd: bool = False,
+        forbid_entities: bool = True,
+        forbid_external: bool = True,
+    ) -> None: ...
+    def defused_start_doctype_decl(
+        self, name, sysid, pubid, has_internal_subset
+    ) -> None: ...
+    def defused_entity_decl(
+        self, name, is_parameter_entity, value, base, sysid, pubid, notation_name
+    ) -> None: ...
+    def defused_unparsed_entity_decl(
+        self, name, base, sysid, pubid, notation_name
+    ) -> None: ...
+    def defused_external_entity_ref_handler(
+        self, context, base, sysid, pubid
+    ) -> None: ...
+    def install(self, parser) -> None: ...
+
+class DefusedExpatBuilderNS(_Namespaces, DefusedExpatBuilder):
+    def install(self, parser) -> None: ...
+    def reset(self) -> None: ...
+
+def parse(
+    file: str | SupportsRead[bytes | str],
+    namespaces: bool = True,
+    forbid_dtd: bool = False,
+    forbid_entities: bool = True,
+    forbid_external: bool = True,
+) -> Document: ...
+def parseString(
+    string: str,
+    namespaces: bool = True,
+    forbid_dtd: bool = False,
+    forbid_entities: bool = True,
+    forbid_external: bool = True,
+) -> Document: ...

mypy-stubs/defusedxml/expatreader.pyi

@@ -0,0 +1,10 @@
+from _typeshed import Incomplete
+
+# Cannot type most things here as DefusedExpatParser is based off of
+# xml.sax.expatreader, which is an undocumented module and lacks types at the moment.
+
+__origin__: str
+
+DefusedExpatParser = Incomplete
+
+def create_parser(*args, **kwargs): ...

mypy-stubs/defusedxml/lxml.pyi

@@ -0,0 +1,53 @@
+import threading
+from _typeshed import Incomplete
+
+# Not bothering with types here as lxml support is supposed to be dropped in a future version
+# of defusedxml
+
+LXML3: Incomplete
+__origin__: str
+tostring: Incomplete
+
+# Should be imported from lxml.etree.ElementBase, but lxml lacks types
+class _ElementBase: ...
+
+class RestrictedElement(_ElementBase):
+    blacklist: Incomplete
+    def __iter__(self): ...
+    def iterchildren(self, tag: Incomplete | None = ..., reversed: bool = ...): ...
+    def iter(self, tag: Incomplete | None = ..., *tags): ...
+    def iterdescendants(self, tag: Incomplete | None = ..., *tags): ...
+    def itersiblings(self, tag: Incomplete | None = ..., preceding: bool = ...): ...
+    def getchildren(self): ...
+    def getiterator(self, tag: Incomplete | None = ...): ...
+
+class GlobalParserTLS(threading.local):
+    parser_config: Incomplete
+    element_class: Incomplete
+    def createDefaultParser(self): ...
+    def setDefaultParser(self, parser) -> None: ...
+    def getDefaultParser(self): ...
+
+getDefaultParser: Incomplete
+
+def check_docinfo(
+    elementtree, forbid_dtd: bool = ..., forbid_entities: bool = ...
+) -> None: ...
+def parse(
+    source,
+    parser: Incomplete | None = ...,
+    base_url: Incomplete | None = ...,
+    forbid_dtd: bool = ...,
+    forbid_entities: bool = ...,
+): ...
+def fromstring(
+    text,
+    parser: Incomplete | None = ...,
+    base_url: Incomplete | None = ...,
+    forbid_dtd: bool = ...,
+    forbid_entities: bool = ...,
+): ...
+
+XML = fromstring
+
+def iterparse(*args, **kwargs) -> None: ...