Add options tests

Add cache tests

Add downloader tests

Add queries tests

Remove redundancy

Add requests tests

Update options

Add interactions tests

Add utils tests

Add CI

Fix final for Python3.7

Try typing extensions

Fix python3.7

[ci skip] Update README.rst

.coveragerc

@@ -0,0 +1,22 @@
+[paths]
+source =
+    omnipath
+    */site-packages/omnipath
+
+[run]
+branch = true
+parallel = true
+source = omnipath
+omit = */__init__.py
+
+[report]
+exclude_lines =
+    \#.*pragma:\s*no.?cover
+
+    if __name__ == .__main__.
+
+    ^\s*raise AssertionError\b
+    ^\s*raise NotImplementedError\b
+    ^\s*return NotImplemented\b
+show_missing = true
+precision = 2

.github/workflows/ci.yml

@@ -0,0 +1,66 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 10
+    strategy:
+      max-parallel: 4
+      matrix:
+        python: [3.7, 3.8]  # , 3.9]
+        os: [ubuntu-latest, macos-latest]
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python }}
+        submodules: false
+
+    - name: Get pip cache dir
+      id: pip-cache
+      run: |
+        echo "::set-output name=dir::$(pip cache dir)"
+
+    - name: Cache pip
+      uses: actions/cache@v2
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox tox-gh-actions codecov
+
+    - name: Linting
+      run: |
+        tox -e lint
+
+    - name: Testing
+      run: |
+        tox
+      env:
+        PLATFORM: ${{ matrix.platform }}
+
+    - name: Upload coverage to Codecov
+      if: success()
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
+      run: |
+        codecov --no-color --required --flags unittests

README.rst

@@ -1,13 +1,8 @@
-|PyPI| |Travis| |Docs|
+|PyPI| |CI| |Docs| |Coverage|
 
 Python client for the OmniPath web service
 ==========================================
 
-**This package is in planning stage, without any useful functionality yet.**
-Contributions are welcome, please contact us at omnipathdb@gmail.com, open
-issues or send pull requests. Otherwise please check out the resources below
-and return to us later.
-
 The OmniPath database
 ---------------------
 
@@ -65,10 +60,14 @@ certain (not all) annotations of the proteins.
     :target: https://pypi.org/project/omnipath
     :alt: PyPI
 
-.. |Travis| image:: https://travis-ci.org/theislab/omnipath.svg?branch=master
-    :target: https://travis-ci.com/github/saezlab/omnipath
+.. |CI| image:: https://img.shields.io/github/workflow/status/michalk8/omnipath/CI/master
+    :target: https://github.com/michalk8/omnipath/actions?query=workflow:CI
     :alt: CI
 
+.. |Coverage| image:: https://codecov.io/gh/michalk8/omnipath/branch/master/graph/badge.svg?token=5A086KQA51
+    :target: https://codecov.io/gh/michalk8/omnipath
+    :alt: Coverage
+
 .. |Docs|  image:: https://img.shields.io/readthedocs/omnipath
     :target: https://omnipath.readthedocs.io/en/latest
     :alt: Documentation

docs/source/index.rst

@@ -1,4 +1,4 @@
-|PyPI| |Travis| |Docs|
+|PyPI| |CI| |Docs| |Coverage|
 
 OmniPath
 ========
@@ -20,13 +20,17 @@ This package is a Python equivalent of an R package `OmnipathR`_ for accessing w
     :target: https://pypi.org/project/omnipath
     :alt: PyPI
 
-.. |Travis| image:: https://travis-ci.org/theislab/omnipath.svg?branch=master
-    :target: https://travis-ci.com/github/saezlab/omnipath
+.. |CI| image:: https://img.shields.io/github/workflow/status/michalk8/omnipath/CI/master
+    :target: https://github.com/michalk8/omnipath/actions?query=workflow:CI
     :alt: CI
 
 .. |Docs|  image:: https://img.shields.io/readthedocs/omnipath
     :target: https://omnipath.readthedocs.io/en/latest
     :alt: Documentation
 
+.. |Coverage| image:: https://codecov.io/gh/michalk8/omnipath/branch/master/graph/badge.svg?token=5A086KQA51
+    :target: https://codecov.io/gh/michalk8/omnipath
+    :alt: Coverage
+
 .. _Saezlab : https://saezlab.org/
 .. _OmniPathR : https://github.com/saezlab/omnipathR

omnipath/__init__.py

@@ -21,6 +21,6 @@
 __full_version__ = (
     f"{__version__}+{__full_version__.local}" if __full_version__.local else __version__
 )
-__server_version__ = _get_server_version()
+__server_version__ = _get_server_version(options)
 
 del parse, version, _get_server_version

omnipath/_core/cache/_cache.py

@@ -125,6 +125,10 @@ def __repr__(self) -> str:
     def __copy__(self) -> "MemoryCache":
         return self
 
+    def copy(self) -> "MemoryCache":
+        """Return self."""
+        return self
+
 
 def clear_cache() -> None:
     """Remove all cached data from :attr:`omnipath.options.cache`."""

omnipath/_core/downloader/_downloader.py

@@ -2,7 +2,6 @@
 from copy import copy
 from typing import Any, Mapping, Callable, Optional
 from hashlib import md5
-from functools import lru_cache
 from urllib.parse import urljoin
 import json
 import logging
@@ -37,15 +36,20 @@ def __init__(self, opts: Optional[Options] = None):
         if opts is None:
             from omnipath import options as opts
 
+        if not isinstance(opts, Options):
+            raise TypeError(
+                f"Expected `opts` to be of type `Options`, found {type(opts).__name__}."
+            )
+
         self._session = Session()
-        self._options = copy(opts)
+        self._options = copy(opts)  # this does not copy MemoryCache
 
         if self._options.num_retries > 0:
             adapter = HTTPAdapter(
                 max_retries=Retry(
                     total=self._options.num_retries,
                     redirect=5,
-                    method_whitelist=["HEAD", "GET", "OPTIONS"],
+                    allowed_methods=["HEAD", "GET", "OPTIONS"],
                     status_forcelist=[413, 429, 500, 502, 503, 504],
                     backoff_factor=1,
                 )
@@ -176,13 +180,10 @@ def __repr__(self) -> str:
         return str(self)
 
 
-@lru_cache()
-def _get_server_version() -> str:
+def _get_server_version(options: Options) -> str:
     """Try and get the server version."""
     import re
 
-    from omnipath import options
-
     def callback(fp: BytesIO) -> str:
         """Parse the version."""
         return re.findall(
@@ -191,7 +192,7 @@ def callback(fp: BytesIO) -> str:
 
     try:
         if not options.autoload:
-            raise ValueError("Autoload is disallowed.")
+            raise ValueError("Autoload is disabled.")
 
         with Options.from_options(
             options,
@@ -209,6 +210,6 @@ def callback(fp: BytesIO) -> str:
                 is_final=False,
             )
     except Exception as e:
-        logging.debug(f"Unable to get server version. Reason `{e}`")
+        logging.debug(f"Unable to get server version. Reason: `{e}`")
 
         return UNKNOWN_SERVER_VERSION

omnipath/_core/query/_query.py

@@ -6,7 +6,6 @@
 
 from omnipath.constants._constants import FormatterMeta, ErrorFormatter
 from omnipath._core.query._query_validator import (
-    DummyValidator,
     EnzsubValidator,
     ComplexesValidator,
     IntercellValidator,
@@ -58,8 +57,7 @@ def __new__(cls, clsname, superclasses, attributedict):  # noqa: D102
             for i, synonym in enumerate(_get_synonyms(k.lower())):
                 attributedict[f"{k}_{i}"] = synonym
 
-        res = super().__new__(cls, clsname, superclasses, attributedict)
-        return res
+        return super().__new__(cls, clsname, superclasses, attributedict)
 
 
 class QueryMeta(SynonymizerMeta, FormatterMeta):  # noqa: D101
@@ -69,13 +67,13 @@ class QueryMeta(SynonymizerMeta, FormatterMeta):  # noqa: D101
 class Query(ErrorFormatter, Enum, metaclass=QueryMeta):  # noqa: D101
     @property
     def _query_name(self) -> str:
-        """Convert synonym to actual query parameter name."""
+        """Convert the synonym to an actual query parameter name."""
         return "_".join(self.name.split("_")[:-1])
 
     @property
-    def _delagate(self):
+    def _delegate(self):
         """Delegate the validation."""
-        return getattr(self.__validator__, self._query_name, DummyValidator)
+        return getattr(self.__validator__, self._query_name)
 
     @property
     def param(self) -> str:
@@ -85,23 +83,23 @@ def param(self) -> str:
     @property
     def valid(self) -> Optional[FrozenSet[str]]:
         """Return the set of valid values for :paramref:`param`."""
-        return self._delagate.valid
+        return self._delegate.valid
 
     @property
     def annotation(self) -> type:
         """Return type annotations for :paramref:`param`."""
-        return self._delagate.annotation
+        return self._delegate.annotation
 
     @property
     def doc(self) -> Optional[str]:
         """Return the docstring for :paramref:`param`."""
-        return self._delagate.doc
+        return self._delegate.doc
 
     def __call__(
         self, value: Optional[Union[str, Sequence[str]]]
     ) -> Optional[Set[str]]:
         """%(validate)s"""  # noqa: D401
-        return self._delagate(value)
+        return self._delegate(value)
 
 
 class EnzsubQuery(Query):  # noqa: D101
@@ -139,5 +137,14 @@ def __call__(
 
     @property
     def endpoint(self) -> str:
-        """Get the API endpoint for this type of query.."""
+        """Get the API endpoint for this type of query."""
         return self.name.lower()
+
+
+__all__ = [
+    EnzsubQuery,
+    InteractionsQuery,
+    ComplexesQuery,
+    AnnotationsQuery,
+    IntercellQuery,
+]