Merge pull request #35 from ldeo-glaciology/change-initialization

Change initialization of package and some renaming of key fns/methods and change the name of everything to xapres

.github/workflows/test.yaml

@@ -35,7 +35,7 @@ jobs:
           # channel-priority: true
           environment-file: ci/environment-py${{ matrix.python-version }}.yml
 
-          activate-environment: test_env_xapres_package
+          activate-environment: test_env_xapres
           use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
       - name: Set up conda environment
         shell: bash -l {0}

README.md

@@ -1,6 +1,8 @@
-# xapres_package
+# xapres
 
-A package for processing data from the Autonomous phase-sensitive Radio-Echo Sounder (ApRES) using xarray. The core ApRES processing code is adapted from code written by Keith Nicholls, British Antarctic Survey, UK. This package uses Keith's code to process the raw ApRES data from autonomous ApRES surveys. It then restructures the data into a convenient format using xarray. This simplifies the challenge of dealing with multiple attenuator and gain settings, makes stacking a straight-forward xarray operation, and allows us to store the large datasets in efficient zarr format in cloud storage. 
+A package for processing data from the Autonomous phase-sensitive Radio-Echo Sounder (ApRES) using xarray. The core ApRES processing code is adapted from code written by Keith Nicholls, British Antarctic Survey, UK. This package uses Keith's code to process the raw ApRES data from ApRES surveys. It then restructures the data into a convenient format using xarray. This simplifies the challenge of dealing with multiple attenuator and gain settings, makes stacking a straight-forward xarray operation, and allows us to store the large datasets in efficient zarr format in cloud storage.
+
+The structure of the resulting xarray depends on if the ApRES data were collected in attended or unattended mode.
 
 ## Installation
 
@@ -16,29 +18,30 @@ The package includes the capability to write data to zarr stores, which can be a
 For example, to lazily access (meaning that no data is downloaded immediately) some recent ApRES data from Greenland, use:
 
 ```
+import xarray as xr
 def reload(site):
     filename = f'gs://ldeo-glaciology/apres/greenland/2022/single_zarrs_noencode/{site}'
     ds = xr.open_dataset(filename,
         engine='zarr', 
         chunks={}) 
     return ds
-A101 = reload("A101')
-A103 = reload("A103')
-A104 = reload("A104')
+A101 = reload("A101")
+A103 = reload("A103")
+A104 = reload("A104")
 ```
 
 Alternatively, you can use a function built-in to the package which loads these data, and also adds some functionality to the xarray it returns: 
 
 ```
-import ApRESDefs as xa
+import xapres as xa
 ds = xa.load_zarr("A101")
 ds
 ```
 
 Now you can compute decibels from a complex profile simply using 
 
 ```
-ds.profile.isel(time=300, chirp_num=0, attenuator_setting_pair=0).db()
+ds.profile.isel(time=300, chirp_num=0, attenuator_setting_pair=0).dB()
 ```
 
 You can also sonify the chirp. Because the frequencies contained in the chirps largely in the audible range, you can play them through the computer's speakers and hear what the ApRES data sound like:

ci/environment-py3.10.yml

@@ -1,4 +1,4 @@
-name: test_env_xapres_package
+name: test_env_xapres
 channels:
   - conda-forge
 dependencies:
@@ -16,6 +16,7 @@ dependencies:
   - gcsfs
   - tqdm
   - pip
+  - zarr
 
 
   ##############

ci/environment-py3.11.yml

@@ -1,4 +1,4 @@
-name: test_env_xapres_package
+name: test_env_xapres
 channels:
   - conda-forge
 dependencies:
@@ -16,6 +16,7 @@ dependencies:
   - gcsfs
   - tqdm
   - pip
+  - zarr
 
 
   ##############

ci/environment-py3.8.yml

@@ -1,4 +1,4 @@
-name: test_env_xapres_package
+name: test_env_xapres
 channels:
   - conda-forge
 dependencies:

ci/environment-py3.9.yml

@@ -1,4 +1,4 @@
-name: test_env_xapres_package
+name: test_env_xapres
 channels:
   - conda-forge
 dependencies:

data/sample/single_dat_file/Untitled.ipynb

@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/Untitled.ipynb

@@ -0,0 +1,134 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "6426f368-9d91-498e-8af3-38d98ee6308c",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'/Users/jkingslake/Documents/science/ApRES/xapres/docs'"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pwd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "f0a0b6ff-3bbf-4164-aaa7-2714c1259047",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "python exec: /Users/jkingslake/mambaforge/envs/xapres_package/bin/python\n",
+      "sys.path: ['/Users/jkingslake/Documents/science/ApRES/xapres_package/docs', '/Users/jkingslake/mambaforge/envs/xapres_package/lib/python311.zip', '/Users/jkingslake/mambaforge/envs/xapres_package/lib/python3.11', '/Users/jkingslake/mambaforge/envs/xapres_package/lib/python3.11/lib-dynload', '', '/Users/jkingslake/mambaforge/envs/xapres_package/lib/python3.11/site-packages']\n"
+     ]
+    },
+    {
+     "ename": "NameError",
+     "evalue": "name '__file__' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[4], line 8\u001b[0m\n\u001b[1;32m      6\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mpython exec:\u001b[39m\u001b[38;5;124m\"\u001b[39m, sys\u001b[38;5;241m.\u001b[39mexecutable)\n\u001b[1;32m      7\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msys.path:\u001b[39m\u001b[38;5;124m\"\u001b[39m, sys\u001b[38;5;241m.\u001b[39mpath)\n\u001b[0;32m----> 8\u001b[0m root \u001b[38;5;241m=\u001b[39m pathlib\u001b[38;5;241m.\u001b[39mPath(\u001b[38;5;18;43m__file__\u001b[39;49m)\u001b[38;5;241m.\u001b[39mparent\u001b[38;5;241m.\u001b[39mparent\u001b[38;5;241m.\u001b[39mabsolute()\n\u001b[1;32m      9\u001b[0m os\u001b[38;5;241m.\u001b[39menviron[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mPYTHONPATH\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mstr\u001b[39m(root)\n\u001b[1;32m     10\u001b[0m sys\u001b[38;5;241m.\u001b[39mpath\u001b[38;5;241m.\u001b[39minsert(\u001b[38;5;241m0\u001b[39m, \u001b[38;5;28mstr\u001b[39m(root))\n",
+      "\u001b[0;31mNameError\u001b[0m: name '__file__' is not defined"
+     ]
+    }
+   ],
+   "source": [
+    "import os\n",
+    "import pathlib\n",
+    "import sys\n",
+    "\n",
+    "\n",
+    "print(\"python exec:\", sys.executable)\n",
+    "print(\"sys.path:\", sys.path)\n",
+    "root = pathlib.Path(__file__).parent.parent.absolute()\n",
+    "os.environ[\"PYTHONPATH\"] = str(root)\n",
+    "sys.path.insert(0, str(root))\n",
+    "\n",
+    "import xapres\n",
+    "\n",
+    "\n",
+    "import xapres  # isort:skip\n",
+    "\n",
+    "# -- Project information -----------------------------------------------------\n",
+    "\n",
+    "project = \"xapres\"\n",
+    "copyright = \"2021, ldeo_glaciology\"\n",
+    "author = \"ldeo_glaciology\"\n",
+    "\n",
+    "# The version info for the project you're documenting, acts as replacement for\n",
+    "# |version| and |release|, also used in various other places throughout the\n",
+    "# built documents.\n",
+    "# see https://pypi.org/project/setuptools-scm/ for details\n",
+    "from pkg_resources import get_distribution\n",
+    "release = get_distribution('xapres').version\n",
+    "# for example take major/minor\n",
+    "version = '.'.join(release.split('.')[:2])\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "6f6a8539-0354-4917-828e-07dde1995bcb",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "PosixPath('.')"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pathlib.Path()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "615c0f3a-7484-4c47-bade-518e9db08746",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/api.rst

@@ -4,7 +4,7 @@
  Example For Autogenerated API Documentation
  ===========================================
 
- .. automodule:: xapres_package.dummy
+ .. automodule:: xapres.dummy
     :members:
     :undoc-members:
     :show-inheritance:

docs/conf.py

@@ -21,11 +21,11 @@
 os.environ["PYTHONPATH"] = str(root)
 sys.path.insert(0, str(root))
 
-import xapres_package  # isort:skip
+import xapres  # isort:skip
 
 # -- Project information -----------------------------------------------------
 
-project = "xapres_package"
+project = "xapres"
 copyright = "2021, ldeo_glaciology"
 author = "ldeo_glaciology"
 
@@ -34,7 +34,7 @@
 # built documents.
 # see https://pypi.org/project/setuptools-scm/ for details
 from pkg_resources import get_distribution
-release = get_distribution('xapres_package').version
+release = get_distribution('xapres').version
 # for example take major/minor
 version = '.'.join(release.split('.')[:2])
 

docs/index.rst

@@ -3,10 +3,10 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to xapres_package's documentation!
+Welcome to xapres's documentation!
 =======================================
 
-This is an awesome description of xapres_package, written in `reStructuredText`_.
+This is an awesome description of xapres, written in `reStructuredText`_.
 
 You can contribute new sections by either adding a new file (see ``new_section.rst``) or just putting a jupyter notebook
 in the ``docs`` folder (see ``new_section_notebook.ipynb``).

environment.yml

@@ -1,4 +1,4 @@
-name: xapres_package
+name: xapres
 channels:
   - conda-forge
 dependencies:
@@ -20,3 +20,4 @@ dependencies:
   - gcsfs
   - tqdm
   - pip
+  - zarr

notebooks/guides/sonify.ipynb

@@ -40,7 +40,7 @@
    "outputs": [],
    "source": [
     "import sys\n",
-    "sys.path.append(\"/Users/jkingslake/Documents/science/ApRES/xapres_package/xapres_package/\")\n",
+    "sys.path.append(\"/Users/jkingslake/Documents/science/ApRES/xapres/xapres/\")\n",
     "import ApRESDefs\n"
    ]
   },