misc

.vscode/settings.json

@@ -0,0 +1,23 @@
+{
+    "workbench.colorCustomizations": {
+        "activityBar.activeBackground": "#68cd21",
+        "activityBar.activeBorder": "#236fdc",
+        "activityBar.background": "#68cd21",
+        "activityBar.foreground": "#15202b",
+        "activityBar.inactiveForeground": "#15202b99",
+        "activityBarBadge.background": "#236fdc",
+        "activityBarBadge.foreground": "#e7e7e7",
+        "sash.hoverBorder": "#68cd21",
+        "statusBar.background": "#52a11a",
+        "statusBar.foreground": "#e7e7e7",
+        "statusBarItem.hoverBackground": "#68cd21",
+        "statusBarItem.remoteBackground": "#52a11a",
+        "statusBarItem.remoteForeground": "#e7e7e7",
+        "titleBar.activeBackground": "#52a11a",
+        "titleBar.activeForeground": "#e7e7e7",
+        "titleBar.inactiveBackground": "#52a11a99",
+        "titleBar.inactiveForeground": "#e7e7e799",
+        "commandCenter.border": "#e7e7e799"
+    },
+    "peacock.color": "#52a11a"
+}

{{ cookiecutter.repo_name }}/README.md

@@ -12,9 +12,6 @@
     │   ├── processed      <- The final, canonical data sets for modeling.
     │   └── raw            <- The original, immutable data dump.
     │
-    ├── docs               <- A default Sphinx project; see sphinx-doc.org for details
-    │
-    ├── models             <- Trained and serialized models, model predictions, or model summaries
     │
     ├── notebooks          <- Jupyter notebooks. Naming convention is a number (for ordering),
     │                         the creator's initials, and a short `-` delimited description, e.g.

{{ cookiecutter.repo_name }}/notebooks/001_001_mjc_EDA.ipynb

@@ -22,7 +22,7 @@
    },
    "outputs": [],
    "source": [
-    "# import your package\n",
+    "# autoreload your package\n",
     "%load_ext autoreload\n",
     "%autoreload 2\n",
     "import {{ cookiecutter.project_name.lower().replace(' ', '_') }}"
@@ -40,10 +40,49 @@
    },
    "outputs": [],
    "source": [
+    "## secrets\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv()  # take environment variables from .env."
+    "load_dotenv()  # take environment variables from .env.\n",
+    "\n",
+    "import warnings\n",
+    "# warnings.simplefilter(\"ignore\")\n",
+    "warnings.filterwarnings(\"ignore\", \".*does not have many workers.*\")\n",
+    "warnings.filterwarnings(\"ignore\", \".*divide by zero.*\")\n",
+    "\n",
+    "## numeric, plotting\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "import matplotlib.pyplot as plt\n",
+    "%matplotlib inline\n",
+    "plt.style.use('ggplot')\n",
+    "plt.rcParams['figure.figsize'] = (7.0, 4)\n",
+    "\n",
+    "## utils\n",
+    "from pathlib import Path\n",
+    "from tqdm.auto import tqdm\n",
+    "import logging, os, re\n",
+    "import collections, functools, itertools\n",
+    "\n",
+    "# torch\n",
+    "import pytorch_lightning as pl\n",
+    "from einops import rearrange, repeat, reduce\n",
+    "import torch\n",
+    "import torch.nn as nn\n",
+    "\n",
+    "# logging\n",
+    "from loguru import logger\n",
+    "logger.remove()\n",
+    "logger.add(os.sys.stdout, level=\"ERROR\", colorize=True, format=\"<level>{time} | {message}</level>\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "54a03c3a",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -55,19 +94,15 @@
     }
    },
    "outputs": [],
-   "source": [
+   "source": []
-    "# I like using ggplot colors\n",
+  },
-    "\n",
+  {
-    "import matplotlib.pyplot as plt\n",
+   "cell_type": "code",
-    "%matplotlib inline\n",
+   "execution_count": null,
-    "plt.style.use('ggplot')\n",
+   "id": "1d4da6fa",
-    "\n",
+   "metadata": {},
-    "import numpy as np\n",
+   "outputs": [],
-    "import pandas as pd\n",
+   "source": []
-    "\n",
-    "from pathlib import Path\n",
-    "from tqdm.auto import tqdm"
-   ]
   },
   {
    "cell_type": "code",
@@ -75,15 +110,7 @@
    "id": "6d102e3d",
    "metadata": {},
    "outputs": [],
-   "source": [
+   "source": []
-    "# and using the logger\n",
-    "import logging\n",
-    "import os\n",
-    "\n",
-    "logging.basicConfig(stream=os.sys.stdout, level=logging.INFO)\n",
-    "logger = logging.getLogger('nb')\n",
-    "logger.setLevel(logging.INFO)"
-   ]
   }
  ],
  "metadata": {

{{ cookiecutter.repo_name }}/requirements/doc_reqs.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+set -e -x
+# This script will document the requirements for multiple conda environments, see ./readme.md for more
+
+# inputs
+PROJECT_NAMES='{{ cookiecutter.python_interpreter }}'
+
+for PROJECT_NAME in $PROJECT_NAMES
+do
+    echo $PROJECT_NAME
+    PYTHON_INTERPRETER=~/miniforge3/envs/$PROJECT_NAME/bin/python
+    # minimal requirement, simpler, but no versions or pip
+    conda env export --no-builds --from-history > requirements/environment.min.yaml
+    # extensive requirements including pip and information overload
+    conda env export > requirements/environment.max.yaml
+    # requirements in a modified pip spec, usefull for dependabot and so on
+    $PYTHON_INTERPRETER -m pip freeze > requirements/conda.requirements.txt
+done
+
+# inputs
+for PROJECT_NAME in $PROJECT_NAMES
+do
+    echo $PROJECT_NAME
+    # conda lock is good for not overspecifying version, but it misses pip
+    cd requirements && conda-lock -f environment.max.yaml -p linux-64
+done

{{ cookiecutter.repo_name }}/requirements/readme.md

@@ -1,6 +1,9 @@
-This project has multiple ways of documenting requirements
+This project has multiple ways of documenting requirements. Since it doesn't cost anything we include them all.
 
 - environment.yaml - This is the manual requirements, use it to install a new test or dev environment
 - environment.min.yaml - This is the minimum requirements, use it to install a new test or dev environment
 - environment.max.yaml - This pins all conda packages, use for production or finding vulnerabilities
-- requirements.txt - For people or bots not using conda
+- conda.requirements.txt - For people or bots not using conda
+
+To update the files run
+`bash requiresments/doc_reqs.sh`