Merge pull request #32 from padraic-shafer/install-extras

Enable pre-commit and install extras

.codecov.yml

@@ -1,4 +1,4 @@
-# show coverage in CI status, not as a comment. 
+# show coverage in CI status, not as a comment.
 comment: off
 coverage:
   status:

.github/CONTRIBUTING.md

@@ -38,10 +38,10 @@ characters.  If the commit is related to a ticket, indicate that with
 "See #3456", "See ticket 3456", "Closes #3456" or similar.
 ```
 
-Describing the motivation for a change, the nature of a bug for bug fixes 
-or some details on what an enhancement does are also good to include in a 
-commit message. Messages should be understandable without looking at the code 
-changes. 
+Describing the motivation for a change, the nature of a bug for bug fixes
+or some details on what an enhancement does are also good to include in a
+commit message. Messages should be understandable without looking at the code
+changes.
 
 Standard acronyms to start the commit message with are:
 ```
@@ -64,7 +64,7 @@ REL: related to releases
 * Now push to your fork
 * Submit a [pull request](https://help.github.com/articles/using-pull-requests) to this branch. This is a start to the conversation.
 
-At this point you're waiting on us. We like to at least comment on pull requests within three business days 
+At this point you're waiting on us. We like to at least comment on pull requests within three business days
 (and, typically, one business day). We may suggest some changes or improvements or alternatives.
 
 Hints to make the integration of your changes easy (and happen faster):

.pre-commit-config.yaml

@@ -2,25 +2,26 @@ default_language_version:
     python: python3
 repos:
   - repo: https://github.com/ambv/black
-    rev: 22.12.0
+    rev: 23.12.1
     hooks:
       - id: black
+        exclude: versioneer.py
   - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 7.0.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.11.2
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["--profile", "black", "--filter-files"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.3.9
+    rev: 0.6.1
     hooks:
       - id: nbstripout

CONTRIBUTING.rst

@@ -101,4 +101,3 @@ Before you submit a pull request, check that it meets these guidelines:
 3. The pull request should work for Python 2.7, 3.3, 3.4, 3.5 and for PyPy. Check
    https://travis-ci.org/bluesky/bluesky-adaptive/pull_requests
    and make sure that the tests pass for all supported Python versions.
-

docker/README.md

@@ -5,7 +5,7 @@ The following docker files are split up for the queue-server and http-server for
 ## To run the containers:
 On a Mac, to use the display you will need to install XQuartz and allow connections from network clients.
 The bash script `local_display.sh` will set up a LOCAL_DISPLAY variable of the host machine and add it to the XQuartz access control list (if needed).
-The queue-monitor gui image is built on [jozo/pyqt5](https://hub.docker.com/r/jozo/pyqt5). 
+The queue-monitor gui image is built on [jozo/pyqt5](https://hub.docker.com/r/jozo/pyqt5).
 
 ```bash
 cd docker/queue-server

docker/queue-monitor/Dockerfile

@@ -1,7 +1,7 @@
 FROM jozo/pyqt5
 
 # Upgrade pip and setuptools
-RUN apt-get update \ 
+RUN apt-get update \
     && apt-get install -y \
     python3-pip \
     python3-setuptools \

docker/queue-monitor/local_display.sh

@@ -19,4 +19,4 @@ fi
 if [[ "$(uname)" == "Darwin" ]]; then
     xhost +"$LOCAL_DISPLAY_IP"
 fi
-export LOCAL_DISPLAY_IP LOCAL_DISPLAY
+export LOCAL_DISPLAY_IP LOCAL_DISPLAY

github_deploy_key_bluesky_bluesky_adaptive.enc

@@ -1 +1 @@
-gAAAAABe9LSqREC-3LuCc4INf-GV0TTSLNuqG07IwzIXVsmvrOp5m7oFKsofOeW4mxu2JghxI-6SWXKYpUfhxmCO5cwEYZ2u0cmDYX_tr6jJWJaIKadWWJFUkAq4VJiwnCm1jhhHEogM_SS20pRaUZA6whoXvBOegAOWzAe0mW8OCP4DxyRXuWlUBeVmitli77sporhJcZ2EUl3e3Z6SBuqZBYABkUhw3_Uct1K2nagJDSz-CKtLmm4bIOmc2NJGFpetT9iI0opUCT3JxtdAhTPVHOosSctxmpt1m3Ds3VIl_rx6tnuHi1HQ5DNpZiMpugAenjoUTNl0hOfFasUjQvaB5n0rk-9w-oo24KtgwHQEox93ZDJWq8s1vc575ekkIkbqGzU9pqNofSUKhmJiABaPYGR_6gmo0t93MnJjnrFMbAQDJ2taLGu5YBd_U3WCK2Jn58mHWnTyWs3nIEvCEjGYaBBuf9xLsWIvc0nvPcY-ALIonpWSfnJS1UgP4JyoIQfLD_GjzDoUhbVleAfCgpKyZciqEb-H_YAtEpyhdU1OxfLAiguDv6aDRT1CGq7wGp5nZQjm_5SXPDv20kx8zVIKUvHKLvzfhAvDQZyHvOVo1jhu7zQxV6p6yyEDxRZ2Xpo5cQJswvVQrE9ZrnfhBqqQ6sObc9tI-ODDBF9thjlKEXToyuHhv5atpcF4hFxnj4CfvCFCicvhSt2oEAQ-Pz8Kvnw7JKVxwPFVYubOsejjuNhvu5p2Eo6VJ_1BhxFZZxFLIYl5ampS1XiH_joAxAiHjQfJCkkB-0BcbYlvIihI0M5cNVTnRT8ZRCsccmXVfONRjRxCwcHJijd8EnJdAIU_OB6gMCbtWx-ZEmg8_YUtuIGL6zOdyvrukHXSlED_0gZiXrDIQywhUMEh-7U1x_SmjgL6Rbybw0fg3LeC3OP73RSYEq25HbJOH6jlEtTXPOb829R9ywzx1pPZVKRETtOhLeBtEEWg54I39T1cOvZnsfCP_3B6C4D0y5JGsaveDo3rUL4j-hluyTJb-67v3jRm3xT_j_envJdL0Zwvtu-9EAJi4vRuTmdL1xaJBGz7RXcZ5ioc-l8WPJIWyf4A-ofxJbQ5MxJtdKxrKfewFXH_zVqFHQV9aAacvxb1StpPb1i0ByFEsXDE-881B2ftnY5zcs8vrD5bxlfvOUIBnt__JBouOAorRGR80BsLEJfuM-SFQTc9Eqsl2c4SQaaMr4ZvbCZlD23Qasn1cvGId09Ko9Ytt85py1jRUn0cA_ePlFcitaC-z2s76gXef9elAeoIuGXJvYAVL8DUFBRTLnL7pNW7IfXzMLGK9xh3QquPBxN8vgI6f0GIBFY3cDIDyuvRClh0NM0Dz1_qgbZfu6CXLnGCdIzJ8IvUWx0v3tf5pH-z0u4_OCYDjdyYV4RIMlGCs_c-RwlMLHjz-JCpNBMvz5d8RvcJ1JRiU5zEZTCVmRBGi6zd7W_UrYWWGZL1xGNtKhSa9_niup5PnZXzooLreZ2p8kgB5YRG8dekNCyOx2-K-2IdZdKkuIA_nG8ql0uPV7FcbvsoZqtVKr6qivPpkSzMWLx9Re8VQPFiEAszoRdfARKgaixmTdwkoM6C5uORCZzLRcRWh_dR3ioz0oleCAwykum1yUZL1sUrdP3Mx1LOeLtT9ZfDhbJhMcJeh3DUCsYFltKHb6TFRWQwkV26D_hkAGU_S_vdktk6_Klet4_OQ-PCtGiTQWze4V71Q5ZeoIwY-eanDV9MNDcvZ3vYeXtHgU7dhBzfto3C1b1p6lRYrCnQ4hO7VM-Lap4trFCsjsgWjs3kIg37S1YokVnph753c7sgNF8maMJukWWRck_5rKWZZ8H7tOdPR3jkWTp8qeqtNLAUuutcgdDTZbSJnzp3i8KMrK8-UBRivDkzdAxwBPxPOkbWEf8yPvwCgGkrwobJ4rLjl6JHydn552WcRrRw_6vtgJVeYJlvvKrFg3LQJvgaZ-A-Hw2Y6Iom3pqaoLzYneMYdj7kTOncCZMCA-G9qRaqhAIKLkUUCdFbeUWd3DwT8qjIIaSFcQ54lY1q9sBwone84q8ww3hKWN7iLzbP4UEC8OFpWzxcjwLy8nUsrdJELtH7kti9O1ioq_Gs1qDTrbig-l_6bddkB9g3HAPFAJXnrjXnyS31a3ZueAzxmOh97-lHuysqtSWCUpm3Dc33leEYt1Tr5wlJXjIe2KqrzK4DMe6L6Bu67SACUDuc4tugLkLWOZlGmytgNVWdbKptBsE6b_ytFTEAiSJVnVMZnUc77zITrYRw2wxkaU2PTIvsfUQz0mj0fN8uItbvZJgv2FT2nbP7ln0bhX9LFko-hJEaESK6pVS0hrVIqCdCVvVvSSfu87f4d-ejA1UQBv8vtq7auEMiE7GQOz8PE4HMOtW_gHicgJw12tuEv_pSSqOw2Q-6e-QgYWxRAN_9iAdZUbWx3R8pll3HvHG_3J_bxVs2JpMcTD3i07o25dmndzsJ_fxTcqnZ-mRfvg0sjEoX5SL1ZET3omTLVHtrh5l8jU6wHtiUX_p5kw42lj7AjxXpJpmd_8lCrywk0EDTR2o7eZJfYjGIr0BsDr0uIBVwag9t4XN9X981o07V7_ypXSJjpsan-L0rApfUwQF8f-3ebnYPGyLzyfD3mrkgZhUF4pHjdB-XEfeEEKZ1H94ZXPZe2tKKMlp7tZ1jkCkmwGQbm-y4z_64cJgDF1dbd77JUjDBY6EqxF-cFYicQErULtNLIBHe_crFJScP9uiSLNsCI-Vi2vXAyk-y07tVrBQFvdpMVMZdZ43RpT-5evIUqtnKfN0PcBWGJ9KkZK901N3Nvv8mFNM3R7ealn6cLXsqaM0EPRpu75vaXYAPuIdqDwgAVzfkv_5f7tKJ5pfnohM0pZs4gqGVt1FR4JgdJqkl67pw5qvUIsi4OCIhErPHgkwxvyoxxxX4HleQN3HII8rmkXax6mh6X0Ej6oUQxVgwotyVulUDLYPFgziQemgyMhTRL14imP3oYbSfrs17Mv86RyqGBYKUhdGlCBDGodiQSegn7yRpE_1ceYJAPLagYuBiETT6YugiNOVE-C2HR9ICTrnLVw8PPFEiMnHDaC46EWhOon5mr0VCiOPXn9SpxxHEXPgC4HWSl2-oZUSAEvaD4afNb-0g3hkmOFEfVD1Siac3YNGcEmR9Q9WvZopi_feVN4KV-PWnhQaOcYYV8Zr4RHuOLQ9jRuh5EeQFeNtaHtqhttmDTxbKXk3P1o4Axg1lWph3HQzjAwHHDF44SwVnfWBr3EXkkTEeuVa4PRTawZvYf18LwjPaqKRAhQf68o9kbYNc4qymGDGNz9G_fNMBFTVsdx7XLLJR9qiWdLEpIRtBuYGN32QAao64gO4-YR7QXkawvRBiEb9HotnHPm737WMYbhMebIZ1jNk75UT6HpS9RwU5vI7kbXu-VxzFAD6w-Y8EYgUni0DXFBmZobk2NXJq489UjB7jasx_ludMcxWxs2SY_pnWJcIgHFsFvbaKLAa-eHxKmfzDOE6BomMvgW9x7meDyHByALsgLSmzsxyioqBuw_CwjwSmxkONNx9ogVkZVtHnm8dg9i1n_9rUmyLIBJ0HMPqZL7tksZ-3EG3E-C2jPnPVMQ2QHOR7ELz0f2-ZqW_5nYgjHGT9f2adE6vPEuLmczUWY73tMVGxnBIf63xak2P4up4RvjW-ECIYTvBE5rdzJ8QcadivHAj1fj_LlbzCQtXtizY_HXPSk-WC1kvngTx7NHCfx8D6gXo34EgZKce9H7a0O5JHFcFNRgYYNx3TnRZQnLAUpqslhiZoYuEI2HVMxAUnuE-kM2xsJ_XixJ52GBE7uIcYPIicsEXyYnD4Y4_I9ivtEDJvI71UC74rCf4wG-BeGOSj7osy_D5OEWNdKeS2ORhMFnIESYrw9oep8b2jSb1qmHSD62wlCCoFVFtbCAumqi5zFcX43LDJgdT1L1p6ecJUoiBLyCVPm32VLy_0WnZV5WGSZeVnkSd2W2Acn74ys5pdOdkDKRpSm5DLuIfB3syvBnpNZvkzlamAjJpzW8pejKz8C0TV0dIh7fHbaTWDJdtPQi7F13nPGlfj8zIixdSJZGY9o-BsePrhCoeiFx-zuPN1oOXG0Z3Fdf4JocvmaoBgKJ9yZr4gLI6Nlr-BlldgEhIlq9JZOKTCdM2VESM9PInqrhnzub0JITNuOySQ8Wn73-cyqYYpfEo3-3PVXo5wVXOxd9LrofIZzrLyaWaAeUR7RRTrFNXxTmp7SrMrqVuLIpGkJRk1aLP1NQUr04qaxAoG_TyivlQAZB_zJCsg07RLGzeFXSEa6po1-ZuVYe0BSZojjLFJY0LliXgFQO1PBFa45wMnILTqt2VJRxKEWvgoPjScFv41ctwZb8I7DutYCK4ypPG0MSMvh9HBJfFUH-Q0MRBH9g==
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requirements-dev.txt

@@ -21,4 +21,4 @@ ophyd
 scipy
 pre-commit
 pytest-docker==1.0.1
-git+https://github.com/bluesky/[email protected]#egg=databroker
+databroker @ git+https://github.com/bluesky/[email protected]#egg=databroker

setup.py

@@ -1,3 +1,4 @@
+import itertools as it
 import sys
 from os import path
 
@@ -31,19 +32,33 @@
     readme = readme_file.read()
 
 
+# fmt: off
+
+
 def read_requirements(filename):
     with open(path.join(here, filename)) as requirements_file:
-        # Parse requirements.txt, ignoring any commented-out lines.
-        requirements = [line for line in requirements_file.read().splitlines() if not line.startswith("#")]
+        # Parse requirements file, ignoring any empty or commented-out lines.
+        requirements = [
+            line for line in requirements_file.read().splitlines()
+            if not (line.startswith("#") or line.strip() == "")
+        ]
     return requirements
 
 
 requirements = read_requirements("requirements.txt")
-categorized_requirements = {key: read_requirements(f"requirements-{key}.txt") for key in ["agents"]}
+categorized_requirements = {
+    key: read_requirements(f"requirements-{key}.txt")
+    for key in ("agents", "dev")
+}
+
+extras_require = categorized_requirements.copy()
+extras_require["all"] = [
+    extra for extra in it.chain.from_iterable(categorized_requirements.values())
+]
+
+
+# fmt: on
 
-extras_require = {}
-extras_require["agents"] = categorized_requirements["agents"]
-extras_require["all"] = categorized_requirements["agents"]
 
 setup(
     name="bluesky-adaptive",