Added changes to docs and notebooks. (#46)

* Add MkDocs. (#41) * Simple MODIS PipeLine Completed. * Working barebones GOES16 Pipeline * Updates. * Quick commit. Co-authored-by: annajungbluth <[email protected]> Co-authored-by: Lilli Freischem <[email protected]> * Coding session w/ Anna & Lilli --------- Co-authored-by: annajungbluth <[email protected]> Co-authored-by: Lilli Freischem <[email protected]> * More Mkdocs. (#42) * Simple MODIS PipeLine Completed. * Working barebones GOES16 Pipeline * Updates. * Quick commit. Co-authored-by: annajungbluth <[email protected]> Co-authored-by: Lilli Freischem <[email protected]> * Coding session w/ Anna & Lilli * Add prelim docs. --------- Co-authored-by: annajungbluth <[email protected]> Co-authored-by: Lilli Freischem <[email protected]> * Updated docs. * Updates. * Final Updates. * Updated the ReadMe. * Fixed pictures. * Fixed links. * Fixed notebooks. * Updated notebooks. * Updates. * Updated requirements and figure. * Updated requirements. * Updates. * Updates. * Updates. * Final Updates. --------- Co-authored-by: annajungbluth <[email protected]> Co-authored-by: Lilli Freischem <[email protected]>
spaceml-org · Jun 3, 2024 · 3cb598f · 3cb598f
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commit 3cb598f
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diff --git a/.env.example b/.env.example
@@ -0,0 +1,5 @@
+ITI_DATA_SAVEDIR=MY/SAVEDIR/
+EARTHDATA_USERNAME=USERNAME
+EARTHDATA_PASSWORD=PASSWORD
+EUMDAC_KEY=KEYYY
+EUMDAC_SECRET=EXAMPLE
diff --git a/Makefile b/Makefile
@@ -2,13 +2,13 @@
 .DEFAULT_GOAL = help
 
 PYTHON = python
-VERSION = 3.10
+VERSION = 3.11
 NAME = py_name
 ROOT = ./
 PIP = pip
 CONDA = conda
 SHELL = bash
-PKGROOT = finitevolx
+PKGROOT = rs_tools
 
 
 help:	## Display this help
@@ -32,5 +32,5 @@ format: ## Code styling - black, isort
 ##@ Testing
 test:  ## Test code using pytest.
 		@printf "\033[1;34mRunning tests with pytest...\033[0m\n\n"
-		pytest -v finitevolx
+		pytest -v rs_tools
 		@printf "\033[1;34mPyTest passes!\033[0m\n\n"
diff --git a/config/miniset/satellite/goes.yaml b/config/miniset/satellite/goes.yaml
@@ -11,10 +11,10 @@ download:
 
 geoprocess:
   _target_: rs_tools._src.geoprocessing.goes.geoprocessor_goes16.geoprocess
-  read_path: /mnt/disks/data/miniset/goes16/raw
-  save_path: /mnt/disks/data/miniset-full-disk/goes16/geoprocessed
+  read_path: ${read_path}/goes16/raw
+  save_path: ${save_path}/goes16/geoprocessed
   resolution: null
-  region: null # "-45 0 -20 40"
+  region: "-45 0 -20 40"
   resample_method: null
 
 patch:

diff --git a/config/miniset/satellite/msg.yaml b/config/miniset/satellite/msg.yaml
@@ -14,7 +14,7 @@ geoprocess:
   read_path: /mnt/disks/data/miniset/msg/raw
   save_path: /mnt/disks/data/miniset-full-disk/msg/geoprocessed
   resolution: null
-  region: null # "-45 0 -20 40"
+  region: "-45 0 -20 40"
   resample_method: null
 
 patch:

diff --git a/docs/index.md b/docs/index.md
@@ -4,7 +4,7 @@
 
 ## What are RS-Tools?
 
-`rs_tools` is a toolbox of functions designed to 
+`rs_tools` is a toolbox of functions designed to handle all of the boilerplate code that comes with preprocessing.
 There is a high barrier to entry when working with remote sensing data for machine learning (ML) research.
 This is especially true for level 1 data which is typically raw radiance observations.
 There are often many domain-specific transformations that can completely make or break the success of the ML task.

diff --git a/docs/pipelines/analysis_datasets.ipynb b/docs/pipelines/analysis_datasets.ipynb
@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 26,
    "id": "86a8d52f-849b-4f0b-a4ea-1e828d51488d",
    "metadata": {},
    "outputs": [
@@ -1894,7 +1894,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

diff --git a/docs/pipelines/goes16.ipynb b/docs/pipelines/goes16.ipynb
diff --git a/docs/pipelines/ml_ready_datasets.ipynb b/docs/pipelines/ml_ready_datasets.ipynb
diff --git a/docs/pipelines/msg.ipynb b/docs/pipelines/msg.ipynb
diff --git a/notebooks/dev/pipelines/1.1-pipeline-goes16.ipynb b/notebooks/dev/pipelines/1.1-pipeline-goes16.ipynb
@@ -5925,7 +5925,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -5939,7 +5939,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.6"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/dev/pipelines/1.2-pipeline-msg.ipynb b/notebooks/dev/pipelines/1.2-pipeline-msg.ipynb
@@ -23,11 +23,14 @@
    "metadata": {},
    "outputs": [
     {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/opt/anaconda3/envs/iti-env/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n"
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'autoroot'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[1], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mautoroot\u001b[39;00m\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mrs_tools\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01m_src\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mutils\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mio\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m get_list_filenames\n\u001b[1;32m      3\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mrioxarray\u001b[39;00m\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'autoroot'"
      ]
     }
    ],
@@ -8837,7 +8840,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "iti-env",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -8851,7 +8854,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

diff --git a/rs_tools/_src/data/goes/downloader_goes16.py b/rs_tools/_src/data/goes/downloader_goes16.py
@@ -109,6 +109,7 @@ def download(
     Returns:
         List[str]: List of downloaded file names
     """
+    logger.debug(f"Save Path: {save_dir}")
     logger.debug(f"TIME STEP: {time_step}")
     # Initialize GOES 16 Downloader
     logger.info("Initializing GOES16 Downloader...")

diff --git a/rs_tools/_src/geoprocessing/goes/geoprocessor_goes16.py b/rs_tools/_src/geoprocessing/goes/geoprocessor_goes16.py
@@ -361,6 +361,8 @@ def geoprocess(
     Returns:
         None
     """
+    logger.debug(f"Read Path: {read_path}")
+    logger.debug(f"Save Path: {save_path}")
     # Initialize GOES 16 GeoProcessor
     logger.info(f"Initializing GOES16 GeoProcessor...")
     # Extracting region from str