first steps towards tests

README.md

@@ -30,4 +30,7 @@ import biobricks as bb
 bb.assets('tox21') # get the paths for the 'tox21' brick
 ```
 
-To list the bricks currently available visit [github.com/biobricks-ai](https://github.com/biobricks-ai)
+To list the bricks currently available visit [github.com/biobricks-ai](https://github.com/biobricks-ai)
+
+# TODO
+1. eventually need to special case (or remove) the testing biobricks token

biobricks/brick.py

@@ -1,10 +1,11 @@
 import subprocess, functools, os, re, datetime, json
 from subprocess import run, DEVNULL
-import types, pyarrow.parquet as pq, re
+import types
 from pathlib import Path
 from .config import bblib, token
 from .logger import logger
-import os, urllib.request as request, functools, dvc.api, shutil
+import os, urllib.request as request, functools, shutil
+# import dvc.api
 from urllib.parse import urlparse
 import sys
 from .checks import check_url_available, check_token, check_symlink_permission, check_safe_git_repo

biobricks/cli.py

@@ -5,7 +5,7 @@
 from importlib import metadata
 
 from .logger import logger
-from .config import read_config, write_config, init_bblib
+from .config import biobricks_config_path, read_config, write_config, init_bblib
 from .checks import check_token
 from .brick import Brick
 from .local_bb import LocalBB
@@ -22,20 +22,22 @@ class Sect:
 @click.option("--bblib", default=None, type=click.Path(), help="path to store bricks")
 @click.option("--token", default=None, help="biobricks.ai/token auth token")
 @click.option("--overwrite", default=False, help="overwrite existing config?")
-def configure(bblib, token, overwrite):
+@click.option("--interactive", default=True, help="run configure interactively?")
+def configure(bblib, token, overwrite, interactive):
+
+    if not interactive:
+        config = { "BBLIB": f"{bblib}", "TOKEN": token }
+        write_config(config)
+        init_bblib()
+        return
 
-    path = Path.home().joinpath(".biobricks")
+    path = biobricks_config_path()
     config = read_config()
 
     # CHECK IF CONFIG WILL OVERWRITE EXISTING
     msg = click.style("WARNING: overwrite existing config?", fg="red")
     if path.exists() and not overwrite and not click.confirm(msg):
         sys.exit(0)
-
-    # EMAIL PROMPT 
-    email = click.prompt("Choose Email", type=click.Path())
-    click.echo("\nRegister and log in to: https://biobricks.ai\nThen copy your token from https://biobricks.ai/token\n")
-    token = click.prompt("Copy token from https://biobricks.ai/token here")
 
     # VALIDATE TOKEN    
     while not check_token(token, silent=True):
@@ -50,7 +52,7 @@ def configure(bblib, token, overwrite):
         bblib = click.prompt("Choose path to store bricks", type=click.Path())
 
     # write configuration
-    config = { "BBLIB": bblib, "TOKEN": token, "EMAIL": email }
+    config = { "BBLIB": bblib, "TOKEN": token }
     write_config(config)
 
     # initialize bblib

biobricks/config.py

@@ -1,20 +1,27 @@
 import os, warnings, json, urllib
 from subprocess import run, DEVNULL, STDOUT
 from pathlib import Path
+import shutil
+
+def biobricks_config_path():
+    return Path.home().joinpath(".biobricks")
 
 def read_config():
-    path = Path.home().joinpath(".biobricks")
+    path = biobricks_config_path()
     if not path.exists(): return {}
     return json.loads(path.read_text())
 
 def write_config(config):
-    path = Path.home().joinpath(".biobricks")
+    path = biobricks_config_path()
     path.write_text(json.dumps(config))
 
 def init_bblib() -> None:
+    breakpoint()
     bbpath = Path(read_config()['BBLIB'])
     os.makedirs(bbpath, exist_ok=True)
     os.makedirs(bbpath / "cache", exist_ok=True)
+    if not shutil.which('git'):
+        raise Exception('Program "git" is not installed. Please install "git"')
     run("git init", cwd=bbpath, stdout=DEVNULL, stderr=STDOUT, shell=True)
     return bblib()
 

changelog.md

@@ -0,0 +1,2 @@
+- remove pyarrow dependency
+- remove git from local_bb

docker/Dockerfile

@@ -1,10 +1,16 @@
 # Create an ubuntu docker image with pip, python, and git
 # build with `docker build -t ubuntu-pip-python-git .`
 # create a container from the image that gets destroyed after use
-# `docker run --rm -it -v ./:/biobricks ubuntu-pip-python-git /bin/bash`
+# `docker run --rm -it -v ./:/home/appuser/biobricks ubuntu-pip-python-git /bin/bash`
 
 FROM python:3.9-slim
 
+# Install system dependencies including Git
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends git && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
 # Install pipx
 RUN python -m pip install --upgrade pip && \
     pip install pipx && \

requirements.txt

@@ -1,4 +1,4 @@
-dvc==2.45.1
 pytest-cov==4.0.0
 click>=8.1.3
-GitPython==3.1.37
+requests>=2.0.0,<3.0.0
+cloup>=3.0.0,<4.0.0

tests/test_init.py

@@ -1,21 +1,39 @@
-# test_cli.py
-import pytest
-from biobricks.cli import register_on_biobricks
+import unittest
+from unittest.mock import patch, MagicMock
+from pathlib import Path
+from biobricks import Brick, cli
+from biobricks.config import write_config, init_bblib
+import tempfile
 
-# Using requests_mock to mock API responses
-@pytest.fixture
-def mock_request(requests_mock):
-    mock_url = 'https://biobricks.ai/api/register'
-    mock_response = {
-        'auth_numbers': '12345',
-        'auth_url': 'https://biobricks.ai/auth'
-    }
-    requests_mock.post(mock_url, json=mock_response, status_code=200)
-    return requests_mock  # This return isn't necessary but can be useful if you want to add more specifics in the fixture.
+def configure(bblib, token, overwrite, interactive):
+
+    if not interactive:
+        config = { "BBLIB": f"{bblib}", "TOKEN": token }
+        write_config(config)
+        init_bblib()
+        return
 
-def test_register_on_biobricks(mock_request):  # This should be the fixture name.
-    result = register_on_biobricks('[email protected]')
+class TestBrickResolve(unittest.TestCase):
+
+    tempdir = tempfile.TemporaryDirectory()
 
-    assert result['message'] == "Authentication needed."
-    assert result['auth_numbers'] == '12345'
-    assert result['auth_url'] == 'https://biobricks.ai/auth'
+    def setUp(self):
+        bblib = Path(f"{TestBrickResolve.tempdir.name}/biobricks")
+        bblib.mkdir(exist_ok=True,parents=True)
+        configure(f"{bblib}", "VQF6Q2U-NKktZ31ioVYa9w", None, None)
+
+    def tearDown(self) -> None:
+        return super().tearDown()
+
+    # test basic install of the hello-brick
+    @patch('biobricks.bblib')
+    def test_install_hello_brick():
+        from biobricks.brick import Brick
+        brick = Brick.Resolve("hello-brick")
+        brick.install()
+        assert brick.path().exists()
+        assert (brick.path() / "hello.txt").exists()
+        assert (brick.path() / "hello.txt").read_text() == "hello world\n"
+
+if __name__ == '__main__':
+    unittest.main()