Merge branch 'release-v0.2.30'

.github/workflows/pythontest.yaml

@@ -29,19 +29,18 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v2
-      - name: Build panoptes-utils image
-        run: |
-          INCLUDE_BASE=true scripts/setup-local-environment.sh
-      - name: Test with pytest in panoptes-utils container
+      - name: Build and test panoptes-utils in container
         run: |
+          docker build -t panoptes-utils:testing -f tests/Dockerfile .
           mkdir -p logs && chmod -R 777 logs
-          PANLOG="${PWD}/logs" SLEEP_TIME=0 scripts/testing/test-software.sh
+          mkdir -p build && chmod -R 777 build
+          docker run --rm -i -v "${PWD}/build:/var/panoptes/panoptes-utils/build" -v "${PWD}/logs:/var/panoptes/logs" panoptes-utils:testing
       - name: Upload coverage report to codecov.io
         uses: codecov/codecov-action@v1
         if: success()
         with:
           name: codecov-upload
-          file: logs/coverage.xml
+          file: build/coverage.xml
           fail_ci_if_error: true
       - name: Create log file artifact
         uses: actions/upload-artifact@v1

.readthedocs.yaml

@@ -9,12 +9,16 @@ version: 2
 sphinx:
   configuration: docs/conf.py
 
-formats: all
+formats: htmlzip
 
 python:
-  version: 3.8
+  version: 3.7
   install:
-    - requirements: docs/requirements.txt
     - method: pip
       path: .
+      extras_requirements:
+        - config
+        - docs
+        - images
+        - social
   system_packages: true

CHANGELOG.rst

@@ -2,8 +2,47 @@
 Changelog
 =========
 
-0.2.29dev
----------
+0.2.30 - 2021-01-14
+-------------------
+
+Added
+^^^^^
+
+* Conda environment file (@wtgee #260)
+* A cli script for ``panoptes-utils``. This will eventually take over the ``panoptes-config-server`` and any other simple commands needed. For now can use ``panoptes-utils tests run`` for building and running tests.
+
+Changed
+^^^^^^^
+
+* Updated testing to use specific docker image. Updated run script for more specific options on starting testing config server. (@wtgee #260)
+* Different ``extras`` install options: ``config``, ``docs``, ``images``, ``testing``, and ``social``. (@wtgee #260)
+* Use ``loguru`` for logging directly in all files, rather than needless import. (@wtgee #260)
+* Make the ``CountdownTimer.sleep()`` less noisy. (#259)
+
+Fixed
+^^^^^
+
+* Plate solving extras option parsing correctly. (@wtgee #260)
+* Explicit imports for some of the utils. (@wtgee #260)
+
+Removed
+^^^^^^^
+
+* Remove Docker services except for testing. (@wtgee #260)
+* Removed unused files: (@wtgee #260)
+
+
+  * Example data fetching notebook removed.
+  * Hotspot script removed.
+  * Data (astrometry index and IERS) download removed.
+  * ``wait-for-it.sh`` script removed.
+  * TheSkyX utils moving to POCS directly.
+  * Removed ``moving_average``.
+  * Removed pipeline functions for getting ``image_id`` and ``sequence_id``.
+
+
+0.2.29 - 2020-10-21
+-------------------
 
 Added
 ^^^^^
@@ -93,7 +132,7 @@ Changed
   * ``stop`` command added that sets ``config_server.running=False`` to break loop.
 
 
-* Testing  (@wtgee #241): 
+* Testing  (@wtgee #241):
 
   * All testing is started from ``scripts/test-software.sh``.
   * The ``panoptes-config-server`` is started as an external service, not in the pytest conf.
@@ -348,7 +387,7 @@ Changed
   * Allow for different RA/Dec column names.
   * Better catalog match function.
 * ``sextractor`` param changes. (#194)
-* **Breaking** ``panoptes.utils.logger`` -> ``panoptes.utils.logger`` so we can ``from panoptes.utils.logging import logger`` (#197)
+* **Breaking** ``panoptes.utils.logger`` -> ``panoptes.utils.logger`` so we can ``from panoptes.utils import logger`` (#197)
 * **Breaking** The ``panoptes.utils.data.assets`` module was removed and the
     ``Downloader`` class is placed directly within the ``scripts/download-data.py`` file. (#197)
 * The ``panopes-utils`` module is not installed in editable mode in the ``latest`` docker image. (#197)

CONTRIBUTING.md

@@ -73,12 +73,12 @@ instead of `My File.py`.
   than using a directory relative imports such as:
   ```python
   from panoptes.utils.base import PanBase
-  from panoptes.utils.utils import current_time
+  from panoptes.utils.time import current_time
   ```
   Import from the top-down instead:
   ```python
   from pocs.base import PanBase
-  from panoptes.utils import current_time
+  from panoptes.utils.time import current_time
   ```
   The same applies to code inside of `peas`.
 - Test imports are slightly different because `pocs/tests` and `peas/tests` are not Python

README.md

@@ -2,7 +2,7 @@ PANOPTES Utilities
 ==================
 
 <p align="center">
-<img src="https://projectpanoptes.org/uploads/2018/12/16/pan-logo.png" alt="PANOPTES logo" />  
+<img src="https://projectpanoptes.org/uploads/2018/12/16/pan-logo.png" alt="PANOPTES logo" />
 </p>
 <br>
 
@@ -12,6 +12,28 @@ Utility functions for use within the [Project PANOPTES](https://projectpanoptes.
 
 This library defines a number of modules that contain useful functions as well as a few services.
 
+Dependencies
+------------
+
+There are a few system dependencies depending on what functionality you will be using.
+
+In particular, the plate solving requires `astrometry.net` and the appropriate index files.
+
+Use the following on a debian-based system (e.g. Ubuntu) to install all dependencies:
+
+```bash
+apt-get update
+
+apt-get install --no-install-recommends --yes \
+  wait-for-it \
+  bzip2 ca-certificates gcc pkg-config \
+  libffi-dev libssl-dev \
+  astrometry.net astrometry-data-tycho2-08 astrometry-data-tycho2 \
+  dcraw exiftool libcfitsio-dev libcfitsio-bin \
+  libfreetype6-dev libpng-dev libjpeg-dev libffi-dev \
+  git
+```
+
 Install
 -------
 
@@ -20,5 +42,11 @@ To install type:
 ```bash
 pip install panoptes-utils
 ```
-
+
+Full options for local install:
+
+```bash
+pip install -e ".[config,docs,images,testing,social]"
+```
+
 See the full documentation at: https://panoptes-utils.readthedocs.io

conftest.py

@@ -9,9 +9,10 @@
 import numpy as np
 import pytest
 from _pytest.logging import caplog as _caplog  # noqa
+from loguru import logger
 from matplotlib import pyplot as plt
+from panoptes.utils.config.server import config_server
 from panoptes.utils.database import PanDB
-from panoptes.utils.logging import logger
 
 _all_databases = ['file', 'memory']
 
@@ -21,10 +22,11 @@
           "<light-blue>{time:MM-DD HH:mm:ss.ss!UTC}</>" \
           "<blue>({time:HH:mm:ss.ss})</> " \
           "| <c>{name} {function}:{line}</c> | " \
-          "<lvl>{message}</lvl>\n"
+          "<lvl>{message}</lvl>"
 
 # Put the log file in the tmp dir.
-log_file_path = os.path.expandvars('${PANLOG}/panoptes-testing.log')
+log_dir = os.getenv('PANLOG', '/var/panoptes/logs')
+log_file_path = os.path.realpath(f'{log_dir}/panoptes-testing.log')
 startup_message = f' STARTING NEW PYTEST RUN - LOGS: {log_file_path} '
 logger.add(log_file_path,
            enqueue=True,  # multiprocessing
@@ -40,6 +42,21 @@
 logger.log('testing', '*' * 25 + startup_message + '*' * 25)
 
 
+def pytest_configure(config):
+    """Set up the testing."""
+    logger.info('Setting up the config server.')
+    config_file = 'tests/testing.yaml'
+
+    host = 'localhost'
+    port = '8765'
+
+    os.environ['PANOPTES_CONFIG_HOST'] = host
+    os.environ['PANOPTES_CONFIG_PORT'] = port
+
+    config_server(config_file, host='localhost', port=8765, load_local=False, save_local=False)
+    logger.success('Config server set up')
+
+
 def pytest_addoption(parser):
     db_names = ",".join(_all_databases) + ' (or all for all databases)'
     group = parser.getgroup("PANOPTES pytest options")
@@ -48,11 +65,6 @@ def pytest_addoption(parser):
         action="store_true",
         default=False,
         help="If tests that require solving should be run")
-    group.addoption(
-        "--theskyx",
-        action="store_true",
-        default=False,
-        help="If running tests alongside a running TheSkyX program.")
     group.addoption(
         "--test-databases",
         nargs="+",
@@ -61,16 +73,6 @@ def pytest_addoption(parser):
               ". Note that travis-ci will test all of them by default."))
 
 
-@pytest.fixture(scope='session')
-def config_host():
-    return os.getenv('PANOPTES_CONFIG_HOST', 'localhost')
-
-
-@pytest.fixture(scope='session')
-def config_port():
-    return os.getenv('PANOPTES_CONFIG_PORT', 6563)
-
-
 @pytest.fixture(scope='session')
 def config_path():
     return os.getenv('PANOPTES_CONFIG_FILE', '/var/panoptes/panoptes-utils/tests/testing.yaml')
@@ -92,7 +94,6 @@ def db_type(request):
 
 @pytest.fixture(scope='function')
 def db(db_type):
-    # TODO don't hardcode the db name.
     return PanDB(db_type=db_type, db_name='panoptes_testing', storage_dir='testing', connect=True)