updated root-level config files

.flake8

@@ -4,8 +4,9 @@ max-line-length = 88
 #     - whitespace after '(' (E201)
 #     - whitespace before ')' (E202)
 #     - whitespace before ':') (E203)
-#     - assigning # to a lambda expression (E371)
+#     - assigning to a lambda expression (E371)
 #     - linebreaking before a binary operator (W503)
-extend-ignore = E201, E202, E203, E731, W503
+#     - multiple statments on one line separated by ';' (E702)
+extend-ignore = E201, E202, E203, E731, W503, E702
 # Ignore config setting files for git, github, intellij, vscode.
-exclude = .git, .github, .idea, .vscode
+extend-exclude = .git, .github, .idea, .vscode

changelog.md

@@ -1 +1,5 @@
-#
+This file contains a curated, chronologically ordered list of notable changes made to aeon_mecha upon each new release. Each bullet point in the list is followed by the accompanying commit hash, and the date of the commit. The versioning numbering used is SemVer. This changelog is based on keep a changelog.
+
+## 0.1.0
+
+- Codebase for interacting with data from experiment 0.1. Will be broken after major refactoring to low-level python api for making file io more generalizable to various different future experiments.

contributing.md

@@ -1 +1 @@
-#
+See the [contributing guidelines in 'aeon_blog'](https://github.com/sainsburyWellcomeCentre/aeon_blog#contributing).

env.yml

@@ -1,42 +1,54 @@
-# Creates a conda environment 'aeon_env' with the required packages
-# run: mamba env create -qf env.yml
-name: aeon_env
+# Python environment yaml setup file
+# run e.g. w/mamba: `mamba env create -qf env.yml`
+
+name: aeon
 channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.9.*
-  - pip
-  - black                  # dev
+  - python>=3.9, <3.10
+  - bandit                                                    # (dev)
+  - black                                                     # (dev)
+  - blas>=1.1, <2
+  - bottleneck>=1.2.1, <2
+  - dotmap
   - fastparquet
-  - flake8                 # dev
+  - flake8                                                    # (dev)
+  - gh                                                        # (dev)
   - graphviz
+  - ipdb                                                      # (dev)
   - ipykernel
-  - isort                  # dev
+  - isort                                                     # (dev)
   - jupyter
   - jupyterlab
   - matplotlib
   - numba>=0.46.0, <1
-  - numpy>=1.21.0
+  - numexpr>=2.6.8, <3
+  - numpy>=1.21.0, <2
+  - opencv
   - pandas>=1.3, <2
+  - pip
   - plotly
   - poetry-core
-  - pre-commit             # dev
+  - pre-commit                                                # (dev)
   - pyarrow
   - pydotplus
   - pymysql
-  - pytest                 # dev
+  - pytest                                                    # (dev)
+  - pytest-cov                                                # (dev)
   - python-graphviz
   - pyyaml
   - scikit-learn
   - scipy
   - seaborn
   - setuptools_scm
+  - sphinx                                                    # (dev)
+  - tox                                                       # (dev)
   - xarray>=0.12.3, <1
-  - pip:
-    - bandit               # dev
-    - datajoint
-    - dotmap
-    - opencv-python
-    - tox                  # dev
-    - git+https://github.com/vathes/datajoint-utilities.git
+  - pip: # Dependencies to install from pypy with `pip`.
+    - datajoint>=0.13, <1
+    - tox
+    - git+https://github.com/vathes/datajoint-utilities.git
+    - git+https://github.com/Technologicat/pyan.git           # (dev)
+
+# note: dev packages can be separated out in a `env_devs.yml` file in future

manifest.in

@@ -1 +1,3 @@
-#
+# We'll use a manifest.in once we're in the stages of building and releasing
+# source distributions:
+# https://packaging.python.org/en/latest/guides/using-manifest-in/