Merge pull request #7 from elixir-europe/test_workflow_branch

Fix docker compose and GitHub actions

.github/workflows/test-mars.yml

@@ -1,36 +1,44 @@
 name: Test MARS
 on:
-    pull_request:
-        paths:
-            -'mars-cli/**'
+  push:
+    paths:
+      - "mars-cli/**"
+  pull_request:
+    paths:
+      - "mars-cli/**"
+    branches:
+      - main
+  workflow_dispatch:
 
 jobs:
-    test-mars:
-        runs-on: ubuntu-latest
-        strategy:
-            matrix:
-                python-version: ["3.9", "3.10", "3.11", "3.12"]
+  test-mars:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    runs-on: ${{ matrix.os }}
+    env:
+      working-directory: ./mars-cli
 
-        steps:
-            - uses: actions/checkout@v4
-            - name: Set up Python
-              uses: actions/setup-python@v4
-              with:
-                python-version: ${{ matrix.python-version }}
-                cache: 'pip'
-
-            - name: Install dependencies
-              run: |
-                python -m pip install --upgrade pip setuptools wheel
-                pip install -r requirements.txt
-                pip install black
-                pip install ruff
-            
-            - name: Test python code
-              run: pytest --doctest-modules --cov=mars_lib tests/ --cov-fail-under=80
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: '**/setup.py'
+      - run: pip install -e '.[test]'
+        working-directory: ${{ env.working-directory }}
+
+      - name: Test python code
+        run: pytest
+        working-directory: ${{ env.working-directory }}
 
-            - name: Formatting
-              run: black --check mars_lib/
+      - name: Formatting
+        run: black --check mars_lib/
+        working-directory: ${{ env.working-directory }}
 
-            - name: Linting
-              run: ruff check mars_lib/
+      - name: Linting
+        run: ruff check mars_lib/
+        working-directory: ${{ env.working-directory }}

mars-cli/.coveragerc

@@ -0,0 +1,2 @@
+[run]
+omit = mars_lib/__init__.py, mars_lib/submit.py, mars_lib/credential.py

mars-cli/README.md

@@ -1,3 +1,18 @@
+# Installing the mars-cli
+
+Installing the mars-cli from source:
+
+```sh
+cd mars-cli # Assuming you are in the root folder
+pip install .
+```
+
+If you want to install the optional testing dependencies as well, useful when contributing to the project:
+
+```sh
+pip install .[test]
+```
+
 # Extending BioSamples' records
 The Python script ``biosamples-externalReferences.py`` defines a class BiosamplesRecord for managing biosample records. This class is designed to interact with the BioSamples database, allowing operations like fetching, updating, and extending biosample records.
 The script takes in a dictionary of BioSamples' accessions and their associated external references, and expands the former with the latter.
@@ -127,4 +142,4 @@ public class BiosamplesIntegration {
         // Handle other operations similarly
     }
 }
-````
+````

mars-cli/mars_lib/credential.py

@@ -1,6 +1,7 @@
 import keyring
 import os
 import getpass
+import keyring.util.platform_ as keyring_platform
 
 """
 Credential Manager Module
@@ -42,22 +43,22 @@
 
 # Don't forget to handle exceptions and secure your credentials properly.
 """
-import keyring.util.platform_ as keyring_platform
 
 print(keyring_platform.config_root())
 # /home/username/.config/python_keyring  # Might be different for you
 
 print(keyring.get_keyring())
 # keyring.backends.SecretService.Keyring (priority: 5)
 
+
 class CredentialManager:
     def __init__(self, service_name):
         self.service_name = service_name
 
     def get_credential_env(self, username):
         """
         Retrieves a credential from environment variables.
-        
+
         :param username: The environment variable username.
         :return: The value of the environment variable or None if not found.
         """
@@ -66,15 +67,15 @@ def get_credential_env(self, username):
     def prompt_for_password(self):
         """
         Securely prompts the user to enter a password in the console.
-        
+
         :return: The password entered by the user.
         """
         return getpass.getpass(prompt="Enter your password: ")
 
     def set_password_keyring(self, username, password):
         """
         Stores a password in the keyring under the given username.
-        
+
         :param username: The username associated with the password.
         :param password: The password to store.
         """
@@ -83,7 +84,7 @@ def set_password_keyring(self, username, password):
     def get_password_keyring(self, username):
         """
         Retrieves a password from the keyring for the given username.
-        
+
         :param username: The username whose password to retrieve.
         :return: The password or None if not found.
         """
@@ -92,8 +93,7 @@ def get_password_keyring(self, username):
     def delete_password_keyring(self, username):
         """
         Deletes a password from the keyring for the given username.
-        
+
         :param username: The username whose password to delete.
         """
         keyring.delete_password(self.service_name, username)
-

mars-cli/pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+addopts = --doctest-modules --cov=mars_lib tests/ --cov-fail-under=80

mars-cli/requirements.txt

@@ -1,3 +1,3 @@
 requests
 jsonschema
-pytest
+keyring

mars-cli/setup.py

@@ -18,6 +18,15 @@
     version=__version__,
     license="MIT",
     install_requires=[required_deps],
+    extras_require={
+        "test": [
+            # Dependencies for testing only
+            "black",
+            "ruff",
+            "pytest",
+            "pytest-cov",
+        ]
+    },
     project_urls={
         "Source": "https://github.com/elixir-europe/MARS",
         "Bug Reports": "https://github.com/elixir-europe/MARS/issues",

repository-services/docker-compose.yml

@@ -1,13 +1,13 @@
-version: '3'
-
 services:
   isa_biosamples:
-      build: ./repository-testservers/isajson-biosamples
+      build: isajson-biosamples
       ports:
         - "8032:8032"
+      restart: unless-stopped
 
   isa_sra:
-      build: ./repository-testservers/isajson-ena
+      build: isajson-ena
       ports:
         - "8042:8042"
+      restart: unless-stopped