Merge pull request #32 from CBroz1/dev

Revise pytesting, update docker, add QC notebook

.gitignore

@@ -30,6 +30,7 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 docker-compose.y*ml
+!docker/docker-compose.y*ml
 
 # C extension, Translations
 # editors: vscode, emacs, Mac
@@ -73,3 +74,4 @@ dj_local_c*.json
 temp*
 *nwb
 **-jvsc-*.py
+/tests/user_data/*

.markdownlint.yaml

@@ -3,13 +3,13 @@
 # https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md
 MD009: false # permit trailing spaces
 MD007: false # List indenting - permit 4 spaces
-MD013: 
+MD013:
     line_length: "88" # Line length limits
     tables: false # disable for tables
     headings: false # disable for headings
 MD030: false # Number of spaces after a list
 MD033: # HTML elements allowed
-    allowed_elements: 
+    allowed_elements:
         - "br"
 MD034: false # Permit bare URLs
 MD031: false # Spacing w/code blocks. Conflicts with `??? Note` and code tab styling

.pre-commit-config.yaml

@@ -1,5 +1,5 @@
 default_stages: [commit, push]
-exclude: (^.github/|^docs/|^images/)
+exclude: (^.github/|^docs/|^images/|^notebooks/py_scripts/)
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -22,6 +22,7 @@ repos:
       - id: black-jupyter
         args:
           - --line-length=88
+          - --exclude=notebooks/py_scripts
 
   # isort
   - repo: https://github.com/pycqa/isort
@@ -54,4 +55,4 @@ repos:
           # W605 - a backslash-character pair that is not a valid escape sequence now
           #        generates a DeprecationWarning. This will eventually become a SyntaxError.
           #        Needed because we use \d as an escape sequence
-          # E402 - Import not at top of file - for notebook scripts
+          # E402 - Import not at top of file - for notebook scripts

CHANGELOG.md

@@ -7,6 +7,9 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 
 + Add - Apply `black` formatting to codebase
 + Update - Move `recursive_search` function
++ Update - Revise Pytests/docker structure
++ Update - Add reference schema for supplemental tables
++ Add - Visualization notebook
 
 ## 0.2.0 - 2022-07-11
 

README.md

@@ -10,6 +10,7 @@ Element is a modular pipeline for data storage and processing with corresponding
 database tables that can be combined with other Elements to assemble a fully functional
 pipeline.
 
-Installation and usage instructions can be found at the [Element documentation](https://datajoint.com/docs/elements/element-miniscope).
+Installation and usage instructions can be found at the
+[Element documentation](https://datajoint.com/docs/elements/element-miniscope).
 
 ![element miniscope diagram](images/attached_miniscope_element.svg)

cspell.json

@@ -0,0 +1,53 @@
+// cSpell Settings
+//https://github.com/streetsidesoftware/vscode-spell-checker
+{
+    "version": "0.2", // Version of the setting file.  Always 0.2
+    "language": "en", // language - current active spelling language
+    "enabledLanguageIds": [
+        "markdown", "yaml"
+    ],
+    // flagWords - list of words to be always considered incorrect
+    // This is useful for offensive words and common spelling errors.
+    // For example "hte" should be "the"
+    "flagWords": [],
+    "allowCompoundWords": true,
+    "ignorePaths": [
+    ],
+    "words": [
+        "Theo",
+        "filt",
+        "djarchive",
+        "tsub",
+        "ssub",
+        "stim",
+        "trialized",
+        "rval",
+        "curations",
+        "npix",
+        "nchannels",
+        "nframes",
+        "nsamples",
+        "neuropil",
+        "POSIX",
+        "deconvolution",
+        "neuro",
+        "pyplot",
+        "imshow",
+        "xpix",
+        "ypix",
+        "dtype",
+        "twinx",
+        "deconvolved",
+        "xlabel",
+        "ylabel",
+        "PSTH",
+        "iterrows",
+        "cmap",
+        "axvline",
+        "axvline",
+        "xlim",
+        "ephys",
+        "tqdm",
+        "Pytests"
+    ]
+}

docker/Dockerfile

@@ -0,0 +1,25 @@
+FROM datajoint/djbase:py3.9-debian-8eb1715
+
+USER anaconda:anaconda
+
+COPY ./workflow-miniscope/docker/apt_requirements.txt /tmp/
+RUN /entrypoint.sh echo "Installed dependencies."
+
+WORKDIR /main/workflow-miniscope
+
+# Always move local - conditional install in setup.sh
+COPY --chown=anaconda:anaconda ./element-lab/ /main/element-lab/
+COPY --chown=anaconda:anaconda ./element-animal/ /main/element-animal/
+COPY --chown=anaconda:anaconda ./element-session/ /main/element-session/
+COPY --chown=anaconda:anaconda ./element-event/ /main/element-event/
+COPY --chown=anaconda:anaconda ./element-interface/ /main/element-interface/
+COPY --chown=anaconda:anaconda ./element-miniscope/ /main/element-miniscope/
+COPY --chown=anaconda:anaconda ./workflow-miniscope/ /main/workflow-miniscope/
+
+# Conditional install - local-all, local-dlc, or git
+COPY --chown=anaconda:anaconda ./workflow-miniscope/docker/setup.sh /main/
+COPY --chown=anaconda:anaconda ./workflow-miniscope/docker/.env /main/
+RUN chmod 755 /main/setup.sh
+RUN chmod 755 /main/.env
+RUN /main/setup.sh
+RUN rm -f ./dj_local_conf.json