diff --git a/Dockerfile b/Dockerfile
index a1557571..8eb84d07 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,5 @@
## Temporary image to build the libraries and only save the needed artifacts
-FROM ghcr.io/osgeo/gdal:ubuntu-full-3.8.3 AS builder
+FROM ghcr.io/osgeo/gdal:ubuntu-small-3.8.4 AS builder
WORKDIR /opt/builder
ARG dataDir=/data
ARG projectDir=/foss_fim
@@ -10,7 +10,7 @@ ENV taudemDir=$depDir/taudem/bin
ENV taudemDir2=$depDir/taudem_accelerated_flowDirections/taudem/build/bin
# remove reference to missing repo
-RUN rm /etc/apt/sources.list.d/apache-arrow.sources
+# RUN rm /etc/apt/sources.list.d/apache-arrow.sources
RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
@@ -45,7 +45,7 @@ RUN cd taudem_accelerated_flowDirections/taudem/build/bin && mv -t $taudemDir2 d
###############################################################################################
# Base Image that has GDAL, PROJ, etc
-FROM ghcr.io/osgeo/gdal:ubuntu-full-3.8.3
+FROM ghcr.io/osgeo/gdal:ubuntu-small-3.8.4
ARG dataDir=/data
ENV projectDir=/foss_fim
ARG depDir=/dependencies
@@ -70,20 +70,12 @@ RUN mkdir -p $depDir
COPY --from=builder $depDir $depDir
# remove reference to missing repo
-RUN rm /etc/apt/sources.list.d/apache-arrow.sources
+# RUN rm /etc/apt/sources.list.d/apache-arrow.sources
-RUN apt-get update --fix-missing && apt-get install -y openjdk-21-jdk && rm -rf /var/lib/apt/lists/*
+RUN apt-get update --fix-missing && rm -rf /var/lib/apt/lists/*
RUN apt update --fix-missing
-# An older version of openjdk still exists on the file system but was never cleaned up
-# After research, we realized, it just needs file cleanup. Leaving it there is triggering security warnings
-# RUN apt-get remove -y openjdk-17-jdk (not installed, just residue left)
-RUN rm -rf ./usr/lib/jvm/*java-1.17* && \
- rm -rf ./usr/lib/jvm/.java-1.17* && \
- rm -rdf ./usr/lib/jvm/java-17*
-
-
-RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt install -y p7zip-full python3-pip time mpich parallel libgeos-dev expect tmux rsync tzdata
+RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt install -y p7zip-full python3-pip time mpich parallel libgeos-dev expect tmux rsync tzdata wget
RUN apt auto-remove
@@ -99,18 +91,15 @@ ENV PYTHONUNBUFFERED=TRUE
## ADD TO PATHS ##
ENV PATH="$projectDir:${PATH}"
-#ENV PATH=${PATH}:$projectDir:$projectDir/$srcDir:$projectDir/tools
-# Jul 17, 2024: Even though PYTHONPATH isn't used, it still seems to want it.
-ENV PYTHONPATH=${PATH}:$srcDir:$projectDir/tools
+ENV PYTHONPATH="${PYTHONPATH}:${projectDir}:${srcDir}:${srcDir}/utils:${projectDir}/data:${toolsDir}"
## install python 3 modules ##
-
COPY Pipfile .
COPY Pipfile.lock .
RUN pip3 install pipenv==2024.0.1 && PIP_NO_CACHE_DIR=off pipenv install --system --deploy --ignore-pipfile
# ----------------------------------
-# Mar 2023
+# Mar 2023 / Sep 2024
# There are some nuances in the whitebox python downloads in that the first time it loads
# it goes to the internet and downloads the latest/greatest WBT (whiteboxtools) engine which is
# required for the whitebox python library to work. We don't want to have FIM attempting a download
@@ -120,12 +109,10 @@ RUN pip3 install pipenv==2024.0.1 && PIP_NO_CACHE_DIR=off pipenv install --syste
# We download and unzip it to the same file folder that pip deployed the whitebox library.
# Whitebox also attempts to always download a folder called testdata regardless of use.
# We added an empty folder to fake out whitebox_tools.py so it doesn't try to download the folder
-
-# RUN wbox_path=/usr/local/lib/python3.10/dist-packages/whitebox/WBT && \
-# wget -P $wbox_path https://www.whiteboxgeo.com/WBT_Linux/WhiteboxTools_linux_musl.zip && \
-# unzip -o $wbox_path/WhiteboxTools_linux_musl.zip -d $wbox_path && \
-# cp $wbox_path/whitebox_tools $wbox_path && \
-# mkdir $wbox_path/testdata
+ENV WBT_PATH=/usr/local/lib/python3.10/dist-packages/whitebox/WBT
+RUN wget -P $WBT_PATH https://www.whiteboxgeo.com/WBT_Linux/WhiteboxTools_linux_musl.zip && \
+ unzip -o $WBT_PATH/WhiteboxTools_linux_musl.zip -d $WBT_PATH && \
+ cp $WBT_PATH/WhiteboxTools_linux_amd64/WBT/whitebox_tools $WBT_PATH
# ----------------------------------
## RUN UMASK TO CHANGE DEFAULT PERMISSIONS ##
diff --git a/Pipfile b/Pipfile
index dd049522..fa068694 100644
--- a/Pipfile
+++ b/Pipfile
@@ -13,7 +13,7 @@ certifi = "==2024.7.4"
dask = "==2024.6.2"
dask-expr = "==1.1.6"
distributed = "==2024.6.2"
-fiona = "==1.9.6"
+fiona = "==1.10.0"
flake8 = "==6.0.0"
flake8-pyproject = "==1.2.3"
geopandas = "==1.0.1"
@@ -21,7 +21,7 @@ gval = "==0.2.7.post1"
ipympl = "==0.9.3"
isort = "==5.12.0"
jupyter = "==1.0.0"
-jupyterlab = "==3.6.7"
+jupyterlab = "==3.6.8"
lmoments3 = "==1.0.6"
monaco = "==0.13.1"
natsort = "==8.3.1"
@@ -50,7 +50,7 @@ seaborn = "==0.12.2"
tables = "==3.8.0"
tqdm = "==4.66.3"
urllib3 = "==1.26.19"
-whitebox = "==2.3.4"
+whitebox = "==2.3.5"
xarray = "==2024.6.0"
zarr = "==2.18.0"
diff --git a/Pipfile.lock b/Pipfile.lock
index 23f15d49..8a570af5 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
{
"_meta": {
"hash": {
- "sha256": "69e8fc55d7092cbd650b00f89e5644b3ef68a4f2ef1a00ec62d5f8645222dae0"
+ "sha256": "5b0ad67893736f5ae7afa8fe3b9f7740f0c53fbda0b0369e4d614609e77b2528"
},
"pipfile-spec": 6,
"requires": {
@@ -24,6 +24,14 @@
"markers": "python_version >= '3.7'",
"version": "==2.4.0"
},
+ "aiobotocore": {
+ "hashes": [
+ "sha256:6d0b4a51d70bc33b1b4eba411076b0cc979aecbdad8e084bab202202423c0725",
+ "sha256:988eef33fd9dd4b070959cfec922278e84166950695b2160bd581623cb6a420c"
+ ],
+ "markers": "python_version >= '3.8'",
+ "version": "==2.15.0"
+ },
"aiofiles": {
"hashes": [
"sha256:1142fa8e80dbae46bb6339573ad4c8c0841358f79c6eb50a493dceca14621bad",
@@ -32,6 +40,127 @@
"markers": "python_version >= '3.7' and python_version < '4.0'",
"version": "==22.1.0"
},
+ "aiohappyeyeballs": {
+ "hashes": [
+ "sha256:55a1714f084e63d49639800f95716da97a1f173d46a16dfcfda0016abb93b6b2",
+ "sha256:7ce92076e249169a13c2f49320d1967425eaf1f407522d707d59cac7628d62bd"
+ ],
+ "markers": "python_version >= '3.8'",
+ "version": "==2.4.0"
+ },
+ "aiohttp": {
+ "hashes": [
+ "sha256:02594361128f780eecc2a29939d9dfc870e17b45178a867bf61a11b2a4367277",
+ "sha256:03f2645adbe17f274444953bdea69f8327e9d278d961d85657cb0d06864814c1",
+ "sha256:074d1bff0163e107e97bd48cad9f928fa5a3eb4b9d33366137ffce08a63e37fe",
+ "sha256:0912b8a8fadeb32ff67a3ed44249448c20148397c1ed905d5dac185b4ca547bb",
+ "sha256:0d277cfb304118079e7044aad0b76685d30ecb86f83a0711fc5fb257ffe832ca",
+ "sha256:0d93400c18596b7dc4794d48a63fb361b01a0d8eb39f28800dc900c8fbdaca91",
+ "sha256:123dd5b16b75b2962d0fff566effb7a065e33cd4538c1692fb31c3bda2bfb972",
+ "sha256:17e997105bd1a260850272bfb50e2a328e029c941c2708170d9d978d5a30ad9a",
+ "sha256:18a01eba2574fb9edd5f6e5fb25f66e6ce061da5dab5db75e13fe1558142e0a3",
+ "sha256:1923a5c44061bffd5eebeef58cecf68096e35003907d8201a4d0d6f6e387ccaa",
+ "sha256:1942244f00baaacaa8155eca94dbd9e8cc7017deb69b75ef67c78e89fdad3c77",
+ "sha256:1b2c16a919d936ca87a3c5f0e43af12a89a3ce7ccbce59a2d6784caba945b68b",
+ "sha256:1c19de68896747a2aa6257ae4cf6ef59d73917a36a35ee9d0a6f48cff0f94db8",
+ "sha256:1e72589da4c90337837fdfe2026ae1952c0f4a6e793adbbfbdd40efed7c63599",
+ "sha256:22c0a23a3b3138a6bf76fc553789cb1a703836da86b0f306b6f0dc1617398abc",
+ "sha256:2c634a3207a5445be65536d38c13791904fda0748b9eabf908d3fe86a52941cf",
+ "sha256:2d21ac12dc943c68135ff858c3a989f2194a709e6e10b4c8977d7fcd67dfd511",
+ "sha256:2f1f1c75c395991ce9c94d3e4aa96e5c59c8356a15b1c9231e783865e2772699",
+ "sha256:305be5ff2081fa1d283a76113b8df7a14c10d75602a38d9f012935df20731487",
+ "sha256:33e6bc4bab477c772a541f76cd91e11ccb6d2efa2b8d7d7883591dfb523e5987",
+ "sha256:349ef8a73a7c5665cca65c88ab24abe75447e28aa3bc4c93ea5093474dfdf0ff",
+ "sha256:380f926b51b92d02a34119d072f178d80bbda334d1a7e10fa22d467a66e494db",
+ "sha256:38172a70005252b6893088c0f5e8a47d173df7cc2b2bd88650957eb84fcf5022",
+ "sha256:391cc3a9c1527e424c6865e087897e766a917f15dddb360174a70467572ac6ce",
+ "sha256:3a1c32a19ee6bbde02f1cb189e13a71b321256cc1d431196a9f824050b160d5a",
+ "sha256:4120d7fefa1e2d8fb6f650b11489710091788de554e2b6f8347c7a20ceb003f5",
+ "sha256:424ae21498790e12eb759040bbb504e5e280cab64693d14775c54269fd1d2bb7",
+ "sha256:44b324a6b8376a23e6ba25d368726ee3bc281e6ab306db80b5819999c737d820",
+ "sha256:4790f0e15f00058f7599dab2b206d3049d7ac464dc2e5eae0e93fa18aee9e7bf",
+ "sha256:4aff049b5e629ef9b3e9e617fa6e2dfeda1bf87e01bcfecaf3949af9e210105e",
+ "sha256:4b38b1570242fbab8d86a84128fb5b5234a2f70c2e32f3070143a6d94bc854cf",
+ "sha256:4d46c7b4173415d8e583045fbc4daa48b40e31b19ce595b8d92cf639396c15d5",
+ "sha256:4f1c9866ccf48a6df2b06823e6ae80573529f2af3a0992ec4fe75b1a510df8a6",
+ "sha256:4f7acae3cf1a2a2361ec4c8e787eaaa86a94171d2417aae53c0cca6ca3118ff6",
+ "sha256:54d9ddea424cd19d3ff6128601a4a4d23d54a421f9b4c0fff740505813739a91",
+ "sha256:58718e181c56a3c02d25b09d4115eb02aafe1a732ce5714ab70326d9776457c3",
+ "sha256:5ede29d91a40ba22ac1b922ef510aab871652f6c88ef60b9dcdf773c6d32ad7a",
+ "sha256:61645818edd40cc6f455b851277a21bf420ce347baa0b86eaa41d51ef58ba23d",
+ "sha256:66bf9234e08fe561dccd62083bf67400bdbf1c67ba9efdc3dac03650e97c6088",
+ "sha256:673f988370f5954df96cc31fd99c7312a3af0a97f09e407399f61583f30da9bc",
+ "sha256:676f94c5480d8eefd97c0c7e3953315e4d8c2b71f3b49539beb2aa676c58272f",
+ "sha256:6c225286f2b13bab5987425558baa5cbdb2bc925b2998038fa028245ef421e75",
+ "sha256:7384d0b87d4635ec38db9263e6a3f1eb609e2e06087f0aa7f63b76833737b471",
+ "sha256:7e2fe37ac654032db1f3499fe56e77190282534810e2a8e833141a021faaab0e",
+ "sha256:7f2bfc0032a00405d4af2ba27f3c429e851d04fad1e5ceee4080a1c570476697",
+ "sha256:7f6b639c36734eaa80a6c152a238242bedcee9b953f23bb887e9102976343092",
+ "sha256:814375093edae5f1cb31e3407997cf3eacefb9010f96df10d64829362ae2df69",
+ "sha256:8224f98be68a84b19f48e0bdc14224b5a71339aff3a27df69989fa47d01296f3",
+ "sha256:898715cf566ec2869d5cb4d5fb4be408964704c46c96b4be267442d265390f32",
+ "sha256:8989f46f3d7ef79585e98fa991e6ded55d2f48ae56d2c9fa5e491a6e4effb589",
+ "sha256:8ba01ebc6175e1e6b7275c907a3a36be48a2d487549b656aa90c8a910d9f3178",
+ "sha256:8c5c6fa16412b35999320f5c9690c0f554392dc222c04e559217e0f9ae244b92",
+ "sha256:8c6a4e5e40156d72a40241a25cc226051c0a8d816610097a8e8f517aeacd59a2",
+ "sha256:8eaf44ccbc4e35762683078b72bf293f476561d8b68ec8a64f98cf32811c323e",
+ "sha256:8fb4fc029e135859f533025bc82047334e24b0d489e75513144f25408ecaf058",
+ "sha256:9093a81e18c45227eebe4c16124ebf3e0d893830c6aca7cc310bfca8fe59d857",
+ "sha256:94c4381ffba9cc508b37d2e536b418d5ea9cfdc2848b9a7fea6aebad4ec6aac1",
+ "sha256:94fac7c6e77ccb1ca91e9eb4cb0ac0270b9fb9b289738654120ba8cebb1189c6",
+ "sha256:95c4dc6f61d610bc0ee1edc6f29d993f10febfe5b76bb470b486d90bbece6b22",
+ "sha256:975218eee0e6d24eb336d0328c768ebc5d617609affaca5dbbd6dd1984f16ed0",
+ "sha256:ad146dae5977c4dd435eb31373b3fe9b0b1bf26858c6fc452bf6af394067e10b",
+ "sha256:afe16a84498441d05e9189a15900640a2d2b5e76cf4efe8cbb088ab4f112ee57",
+ "sha256:b1c43eb1ab7cbf411b8e387dc169acb31f0ca0d8c09ba63f9eac67829585b44f",
+ "sha256:b90078989ef3fc45cf9221d3859acd1108af7560c52397ff4ace8ad7052a132e",
+ "sha256:b98e698dc34966e5976e10bbca6d26d6724e6bdea853c7c10162a3235aba6e16",
+ "sha256:ba5a8b74c2a8af7d862399cdedce1533642fa727def0b8c3e3e02fcb52dca1b1",
+ "sha256:c31ad0c0c507894e3eaa843415841995bf8de4d6b2d24c6e33099f4bc9fc0d4f",
+ "sha256:c3b9162bab7e42f21243effc822652dc5bb5e8ff42a4eb62fe7782bcbcdfacf6",
+ "sha256:c58c6837a2c2a7cf3133983e64173aec11f9c2cd8e87ec2fdc16ce727bcf1a04",
+ "sha256:c83f7a107abb89a227d6c454c613e7606c12a42b9a4ca9c5d7dad25d47c776ae",
+ "sha256:cde98f323d6bf161041e7627a5fd763f9fd829bcfcd089804a5fdce7bb6e1b7d",
+ "sha256:ce91db90dbf37bb6fa0997f26574107e1b9d5ff939315247b7e615baa8ec313b",
+ "sha256:d00f3c5e0d764a5c9aa5a62d99728c56d455310bcc288a79cab10157b3af426f",
+ "sha256:d17920f18e6ee090bdd3d0bfffd769d9f2cb4c8ffde3eb203777a3895c128862",
+ "sha256:d55f011da0a843c3d3df2c2cf4e537b8070a419f891c930245f05d329c4b0689",
+ "sha256:d742c36ed44f2798c8d3f4bc511f479b9ceef2b93f348671184139e7d708042c",
+ "sha256:d9a487ef090aea982d748b1b0d74fe7c3950b109df967630a20584f9a99c0683",
+ "sha256:d9ef084e3dc690ad50137cc05831c52b6ca428096e6deb3c43e95827f531d5ef",
+ "sha256:da452c2c322e9ce0cfef392e469a26d63d42860f829026a63374fde6b5c5876f",
+ "sha256:dc4826823121783dccc0871e3f405417ac116055bf184ac04c36f98b75aacd12",
+ "sha256:de7a5299827253023c55ea549444e058c0eb496931fa05d693b95140a947cb73",
+ "sha256:e04a1f2a65ad2f93aa20f9ff9f1b672bf912413e5547f60749fa2ef8a644e061",
+ "sha256:e1ca1ef5ba129718a8fc827b0867f6aa4e893c56eb00003b7367f8a733a9b072",
+ "sha256:ee40b40aa753d844162dcc80d0fe256b87cba48ca0054f64e68000453caead11",
+ "sha256:f071854b47d39591ce9a17981c46790acb30518e2f83dfca8db2dfa091178691",
+ "sha256:f29930bc2921cef955ba39a3ff87d2c4398a0394ae217f41cb02d5c26c8b1b77",
+ "sha256:f489a2c9e6455d87eabf907ac0b7d230a9786be43fbe884ad184ddf9e9c1e385",
+ "sha256:f5bf3ead3cb66ab990ee2561373b009db5bc0e857549b6c9ba84b20bc462e172",
+ "sha256:f6f18898ace4bcd2d41a122916475344a87f1dfdec626ecde9ee802a711bc569",
+ "sha256:f8112fb501b1e0567a1251a2fd0747baae60a4ab325a871e975b7bb67e59221f",
+ "sha256:fd31f176429cecbc1ba499d4aba31aaccfea488f418d60376b911269d3b883c5"
+ ],
+ "markers": "python_version >= '3.8'",
+ "version": "==3.10.5"
+ },
+ "aioitertools": {
+ "hashes": [
+ "sha256:c2a9055b4fbb7705f561b9d86053e8af5d10cc845d22c32008c43490b2d8dd6b",
+ "sha256:fc1f5fac3d737354de8831cbba3eb04f79dd649d8f3afb4c5b114925e662a796"
+ ],
+ "markers": "python_version >= '3.8'",
+ "version": "==0.12.0"
+ },
+ "aiosignal": {
+ "hashes": [
+ "sha256:54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc",
+ "sha256:f8376fb07dd1e86a584e4fcdec80b36b7f81aac666ebc724e2c090300dd83b17"
+ ],
+ "markers": "python_version >= '3.7'",
+ "version": "==1.3.1"
+ },
"aiosqlite": {
"hashes": [
"sha256:36a1deaca0cac40ebe32aac9977a6e2bbc7f5189f23f4a54d5908986729e5bd6",
@@ -42,11 +171,11 @@
},
"anyio": {
"hashes": [
- "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94",
- "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"
+ "sha256:c5a275fe5ca0afd788001f58fca1e69e29ce706d746e317d660e21f70c530ef9",
+ "sha256:fdeb095b7cc5a5563175eedd926ec4ae55413bb4be5770c424af0ba46ccb4a78"
],
"markers": "python_version >= '3.8'",
- "version": "==4.4.0"
+ "version": "==4.5.0"
},
"appdirs": {
"hashes": [
@@ -111,6 +240,14 @@
],
"version": "==2.4.1"
},
+ "async-timeout": {
+ "hashes": [
+ "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f",
+ "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"
+ ],
+ "markers": "python_version < '3.11'",
+ "version": "==4.0.3"
+ },
"attrs": {
"hashes": [
"sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346",
@@ -210,11 +347,11 @@
},
"botocore": {
"hashes": [
- "sha256:bce42967d0f03b79cf25b2b6a36221fb2fb15f98e6fa4155b66b672ab192013b",
- "sha256:e599cef6305e950a212f85adb86c1f4713d4b2678b3c2ec54df6b8e2dbe9ef2f"
+ "sha256:1b48c94e8a4bbe23143f3d1c21a32b9ffc7476b651ef42371ab45d678f6dbfbc",
+ "sha256:3564a980d95ff2861a6ca74313173d8778aa659125c63cf49c93ad23896c63b1"
],
"markers": "python_version >= '3.8'",
- "version": "==1.35.1"
+ "version": "==1.35.16"
},
"bottleneck": {
"hashes": [
@@ -371,76 +508,76 @@
},
"cffi": {
"hashes": [
- "sha256:011aff3524d578a9412c8b3cfaa50f2c0bd78e03eb7af7aa5e0df59b158efb2f",
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],
"markers": "python_version >= '3.8'",
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+ "version": "==1.17.1"
},
"cfgv": {
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@@ -631,53 +768,74 @@
},
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- "sha256:fe0ccca550bb8e5abc22f530ec0466136379c01321fd94f30a22231e8a48d985"
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+ "sha256:3faeb2998e4fcb256542e8a926d08da08977f7f5e62cf733f3c211c2a5586223",
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+ "sha256:68a32389b06b82c2fdd68276148d7b9275b5f5cf13e5417e4252f6d1a34f72a2",
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+ "sha256:81cb5ed4952aae6014bc9d0421dec7c5835c9c8c31cdf51910b708f548cf58e5",
+ "sha256:834e0cfe17ba12f79963861e0f908556b2cedd52e1f75e6578801febcc6a9f49",
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+ "sha256:94e848a6b83da10898cbf1311a815f770acc9b6a3f2d646f330d57eb4e87592e",
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+ "sha256:a11077e395f67ffc2c44ec2418cfebed032cd6da3022a94fc227b6faf8e2acb8",
+ "sha256:aea348f053c645100612b333adc5983d87be69acdc6d77d3169c090d3b01dc35",
+ "sha256:b11b39aea6be6764f84360fce6c82211a9db32a7c7de8fa6dd5397cf1d079c3b",
+ "sha256:c6c7c2408b7048082932cf4e641fa3b8ca848259212f51c8c59c45aa7ac18f14",
+ "sha256:c6ec93afeb848a0845a18989da3beca3eec2c0f852322efe21af1931147d12cb",
+ "sha256:cacd81e2d4b6f89c9f8a5b69b86490152ff39afc58a95af002a398273e5ce589",
+ "sha256:d402880b84df3bec6eab53cd0cf802cae6a2ef9537e70cf75e91618a3801c20c",
+ "sha256:d51fca85f9f7ad0b65b4b9fe800406d0d77017d7270d31ec3fb1cc07358fdea0",
+ "sha256:d73f659398a0904e125280836ae6f88ba9b178b2fed6884f3b1f95b989d2c8da",
+ "sha256:d78ab28a03c854a873787a0a42254a0ccb3cb133c672f645c9f9c8f3ae9d0800",
+ "sha256:da84c537cb8b97d153e9fb208c221c45605f73147bd4cadd23bdae915042aad6",
+ "sha256:dbc4c3217eee163fa3984fd1567632b48d6dfd29216da3ded3d7b844a8014a66",
+ "sha256:e12968fdfd5bb45ffdf6192a590bd8ddd3ba9e58360b29683c6bb71a7b41edca",
+ "sha256:e1fd23e9d01591bab45546c089ae89d926917a66dceb3abcf01f6105d927e2cb",
+ "sha256:e8134301d7e204c88ed7ab50028ba06c683000040ede1d617298611f9dc6240c",
+ "sha256:eb8b141bb00fa977d9122636b16aa67d37fd40a3d8b52dd837e536d64b9a4d06",
+ "sha256:eca7e17a65f72a5133bdbec9ecf22401c62bcf4821361ef7811faee695799779",
+ "sha256:f317576606de89da6b7e0861cf6061f6146ead3528acabff9236458a6ba467f8",
+ "sha256:fd2a0fc506eccaaa7595b7e1418951f213cf8255be2600f1ea1b61e46a60c55f",
+ "sha256:fe41b41505a5a33aeaed2a613dccaeaa74e0e3ead6dd6fd3a118fb471644fd6c"
],
"markers": "python_version >= '3.9'",
- "version": "==1.2.1"
+ "version": "==1.3.0"
},
"cycler": {
"hashes": [
@@ -866,11 +1024,11 @@
},
"executing": {
"hashes": [
- "sha256:35afe2ce3affba8ee97f2d69927fa823b08b472b7b994e36a52a964b93d16147",
- "sha256:eac49ca94516ccc753f9fb5ce82603156e590b27525a8bc32cce8ae302eb61bc"
+ "sha256:8d63781349375b5ebccc3142f4b30350c0cd9c79f921cde38be2be4637e98eaf",
+ "sha256:8ea27ddd260da8150fa5a708269c4a10e76161e2496ec3e587da9e3c0fe4b9ab"
],
- "markers": "python_version >= '3.5'",
- "version": "==2.0.1"
+ "markers": "python_version >= '3.8'",
+ "version": "==2.1.0"
},
"fasteners": {
"hashes": [
@@ -889,42 +1047,43 @@
},
"filelock": {
"hashes": [
- "sha256:2207938cbc1844345cb01a5a95524dae30f0ce089eba5b00378295a17e3e90cb",
- "sha256:6ca1fffae96225dab4c6eaf1c4f4f28cd2568d3ec2a44e15a08520504de468e7"
+ "sha256:2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0",
+ "sha256:c249fbfcd5db47e5e2d6d62198e565475ee65e4831e2561c8e313fa7eb961435"
],
"markers": "python_version >= '3.8'",
- "version": "==3.15.4"
+ "version": "==3.16.1"
},
"fiona": {
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+ "sha256:d99d2faa8cb3590dc0018a2832af39e1930b39cfff53017f3681d505bf813fee",
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+ "sha256:ef44b3b0704244503a5f12ae92ca88b2cf4fedc9fd881b00c7c58b6899ca5133",
+ "sha256:f335beb927c5e9d9997a9cf665d6eee2e24191a02582f01786afa76119b71110"
],
"index": "pypi",
- "markers": "python_version >= '3.7'",
- "version": "==1.9.6"
+ "markers": "python_version >= '3.8'",
+ "version": "==1.10.0"
},
"flake8": {
"hashes": [
@@ -1006,13 +1165,96 @@
],
"version": "==1.5.1"
},
+ "frozenlist": {
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+ ],
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+ },
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- "sha256:fad7d7e209dd4c1208e3bbfda706620e0da5142bebbd9c384afb95b07e798e49"
+ "sha256:6271f1d3075a378bfe432f6f42bf7e1d2a6ba74f78dd9b512385474c579146a0",
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],
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- "version": "==2024.6.1"
+ "version": "==2023.12.1"
},
"geocube": {
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@@ -1058,27 +1300,27 @@
},
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],
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+ "version": "==2.6.1"
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],
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- "version": "==3.7"
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+ "version": "==3.10"
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@@ -1157,11 +1399,11 @@
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@@ -1172,11 +1414,11 @@
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@@ -1311,11 +1553,11 @@
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@@ -1343,12 +1585,12 @@
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@@ -1368,121 +1610,131 @@
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},
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@@ -1691,65 +1943,171 @@
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+ "sha256:ff3827aef427c89a25cc96ded1759271a93603aba9fb977a6d264648ebf989db"
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"markers": "python_version >= '3.8'",
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+ "version": "==6.1.0"
},
"multimethod": {
"hashes": [
@@ -2223,11 +2581,11 @@
},
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+ "version": "==4.3.6"
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@@ -2529,52 +2887,52 @@
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+ "version": "==1.10.18"
},
"pyflakes": {
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@@ -2636,11 +2994,11 @@
},
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},
"pyppmd": {
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@@ -2806,10 +3164,10 @@
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@@ -2872,118 +3230,118 @@
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+ "version": "==26.2.0"
},
"pyzstd": {
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@@ -3082,11 +3440,11 @@
},
"qtconsole": {
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],
"markers": "python_version >= '3.8'",
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},
"qtpy": {
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@@ -3364,11 +3722,11 @@
},
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+ "markers": "python_version >= '3.8'",
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},
"s3transfer": {
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@@ -3380,30 +3738,30 @@
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- "sha256:1ff4ba34c2abff5ec59c803ed1d97d61b036f659a17f55be102679e88f926fac",
- "sha256:508907e5f81390e16d754e8815f7497e52139162fd69c4fdbd2dfa5d6cc88915",
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- "sha256:689b6f74b2c880276e365fe84fe4f1befd6a774f016339c65655eaff12e10cbf",
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- "sha256:7b073a27797a283187a4ef4ee149959defc350b46cbf63a84d8514fe16b69855",
- "sha256:88e0672c7ac21eb149d409c74cc29f1d611d5158175846e7a9c2427bd12b3956",
- "sha256:909144d50f367a513cee6090873ae582dba019cb3fca063b38054fa42704c3a4",
- "sha256:97625f217c5c0c5d0505fa2af28ae424bd37949bb2f16ace3ff5f2f81fb4498b",
- "sha256:9a07f90846313a7639af6a019d849ff72baadfa4c74c778821ae0fad07b7275b",
- "sha256:b59e3e62d2be870e5c74af4e793293753565c7383ae82943b83383fdcf5cc5c1",
- "sha256:b5e865e9bd59396220de49cb4a57b17016256637c61b4c5cc81aaf16bc123bbe",
- "sha256:da3f404e9e284d2b0a157e1b56b6566a34eb2798205cba35a211df3296ab7a74",
- "sha256:f5b213bc29cc30a89a3130393b0e39c847a15d769d6e59539cd86b75d276b1a7"
+ "sha256:03b6158efa3faaf1feea3faa884c840ebd61b6484167c711548fce208ea09445",
+ "sha256:1ff45e26928d3b4eb767a8f14a9a6efbf1cbff7c05d1fb0f95f211a89fd4f5de",
+ "sha256:299406827fb9a4f862626d0fe6c122f5f87f8910b86fe5daa4c32dcd742139b6",
+ "sha256:2d4cad1119c77930b235579ad0dc25e65c917e756fe80cab96aa3b9428bd3fb0",
+ "sha256:394397841449853c2290a32050382edaec3da89e35b3e03d6cc966aebc6a8ae6",
+ "sha256:3a686885a4b3818d9e62904d91b57fa757fc2bed3e465c8b177be652f4dd37c8",
+ "sha256:3b923d119d65b7bd555c73be5423bf06c0105678ce7e1f558cb4b40b0a5502b1",
+ "sha256:3bed4909ba187aca80580fe2ef370d9180dcf18e621a27c4cf2ef10d279a7efe",
+ "sha256:52788f48b5d8bca5c0736c175fa6bdaab2ef00a8f536cda698db61bd89c551c1",
+ "sha256:57cc1786cfd6bd118220a92ede80270132aa353647684efa385a74244a41e3b1",
+ "sha256:643964678f4b5fbdc95cbf8aec638acc7aa70f5f79ee2cdad1eec3df4ba6ead8",
+ "sha256:6c16d84a0d45e4894832b3c4d0bf73050939e21b99b01b6fd59cbb0cf39163b6",
+ "sha256:757c7d514ddb00ae249832fe87100d9c73c6ea91423802872d9e74970a0e40b9",
+ "sha256:8c412ccc2ad9bf3755915e3908e677b367ebc8d010acbb3f182814524f2e5540",
+ "sha256:b4237ed7b3fdd0a4882792e68ef2545d5baa50aca3bb45aa7df468138ad8f94d",
+ "sha256:c15b1ca23d7c5f33cc2cb0a0d6aaacf893792271cddff0edbd6a40e8319bc113",
+ "sha256:ca64b3089a6d9b9363cd3546f8978229dcbb737aceb2c12144ee3f70f95684b7",
+ "sha256:f60021ec1574e56632be2a36b946f8143bf4e5e6af4a06d85281adc22938e0dd",
+ "sha256:f763897fe92d0e903aa4847b0aec0e68cadfff77e8a0687cabd946c89d17e675",
+ "sha256:f8b0ccd4a902836493e026c03256e8b206656f91fbcc4fde28c57a5b752561f1",
+ "sha256:f932a02c3f4956dfb981391ab24bda1dbd90fe3d628e4b42caef3e041c67707a"
],
"markers": "python_version >= '3.9'",
- "version": "==1.5.1"
+ "version": "==1.5.2"
},
"scipy": {
"hashes": [
@@ -3456,11 +3814,11 @@
},
"setuptools": {
"hashes": [
- "sha256:3c08705fadfc8c7c445cf4d98078f0fafb9225775b2b4e8447e40348f82597c0",
- "sha256:f2bfcce7ae1784d90b04c57c2802e8649e1976530bb25dc72c2b078d3ecf4864"
+ "sha256:35ab7fd3bcd95e6b7fd704e4a1539513edad446c097797f2985e0e4b960772f2",
+ "sha256:d59a21b17a275fb872a9c3dae73963160ae079f1049ed956880cd7c09b120538"
],
"markers": "python_version >= '3.8'",
- "version": "==73.0.0"
+ "version": "==75.1.0"
},
"shapely": {
"hashes": [
@@ -3790,11 +4148,11 @@
},
"types-python-dateutil": {
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- "sha256:5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202",
- "sha256:6b8cb66d960771ce5ff974e9dd45e38facb81718cc1e208b10b1baccbfdbee3b"
+ "sha256:27c8cc2d058ccb14946eebcaaa503088f4f6dbc4fb6093d3d456a49aef2753f6",
+ "sha256:9706c3b68284c25adffc47319ecc7947e5bb86b3773f843c73906fd598bc176e"
],
"markers": "python_version >= '3.8'",
- "version": "==2.9.0.20240316"
+ "version": "==2.9.0.20240906"
},
"typing-extensions": {
"hashes": [
@@ -3837,11 +4195,11 @@
},
"virtualenv": {
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- "sha256:4c43a2a236279d9ea36a0d76f98d84bd6ca94ac4e0f4a3b9d46d05e10fea542a",
- "sha256:8cc4a31139e796e9a7de2cd5cf2489de1217193116a8fd42328f1bd65f434589"
+ "sha256:4f3ac17b81fba3ce3bd6f4ead2749a72da5929c01774948e243db9ba41df4ff6",
+ "sha256:ce489cac131aa58f4b25e321d6d186171f78e6cb13fafbf32a840cee67733ff4"
],
"markers": "python_version >= '3.7'",
- "version": "==20.26.3"
+ "version": "==20.26.5"
},
"wcwidth": {
"hashes": [
@@ -3874,19 +4232,19 @@
},
"whitebox": {
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- "sha256:3479c8127b1928dd0457b6680b9ee4469d0735b2bb220178c678af303d868ef0",
- "sha256:4322c5a3b42f1f04a3c80640253b672242e0aefb6b6dea70752f00a220f6d7ed"
+ "sha256:4a9fb6da799dc0f99daf139d6dbe573ca12af3785c48708e56728b8372c6a2a7",
+ "sha256:dd9db85bbb687356741afe935dd25286a2b31e7bf87b74c60b655cdf84a9d922"
],
"index": "pypi",
- "version": "==2.3.4"
+ "version": "==2.3.5"
},
"widgetsnbextension": {
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- "sha256:8b22a8f1910bfd188e596fe7fc05dcbd87e810c8a4ba010bdb3da86637398474"
+ "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71",
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],
"markers": "python_version >= '3.7'",
- "version": "==4.0.11"
+ "version": "==4.0.13"
},
"wrapt": {
"hashes": [
@@ -3991,11 +4349,11 @@
},
"xyzservices": {
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- "sha256:fecb2508f0f2b71c819aecf5df2c03cef001c56a4b49302e640f3b34710d25e4"
+ "sha256:68fb8353c9dbba4f1ff6c0f2e5e4e596bb9e1db7f94f4f7dfbcb26e25aa66fde",
+ "sha256:776ae82b78d6e5ca63dd6a94abb054df8130887a4a308473b54a6bd364de8644"
],
"markers": "python_version >= '3.8'",
- "version": "==2024.6.0"
+ "version": "==2024.9.0"
},
"y-py": {
"hashes": [
@@ -4076,6 +4434,104 @@
],
"version": "==0.6.2"
},
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+ "sha256:f61db3b7e870914dbd9434b560075e0366771eecbe6d2b5561f5bc7485f39efd"
+ ],
+ "markers": "python_version >= '3.8'",
+ "version": "==1.11.1"
+ },
"ypy-websocket": {
"hashes": [
"sha256:43a001473f5c8abcf182f603049cf305cbc855ad8deaa9dfa0f3b5a7cea9d0ff",
@@ -4103,11 +4559,11 @@
},
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- "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"
+ "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350",
+ "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"
],
"markers": "python_version >= '3.8'",
- "version": "==3.20.0"
+ "version": "==3.20.2"
}
},
"develop": {
@@ -4136,19 +4592,19 @@
},
"executing": {
"hashes": [
- "sha256:35afe2ce3affba8ee97f2d69927fa823b08b472b7b994e36a52a964b93d16147",
- "sha256:eac49ca94516ccc753f9fb5ce82603156e590b27525a8bc32cce8ae302eb61bc"
+ "sha256:8d63781349375b5ebccc3142f4b30350c0cd9c79f921cde38be2be4637e98eaf",
+ "sha256:8ea27ddd260da8150fa5a708269c4a10e76161e2496ec3e587da9e3c0fe4b9ab"
],
- "markers": "python_version >= '3.5'",
- "version": "==2.0.1"
+ "markers": "python_version >= '3.8'",
+ "version": "==2.1.0"
},
"ipython": {
"hashes": [
- "sha256:1cec0fbba8404af13facebe83d04436a7434c7400e59f47acf467c64abd0956c",
- "sha256:e6b347c27bdf9c32ee9d31ae85defc525755a1869f14057e900675b9e8d6e6ff"
+ "sha256:0b99a2dc9f15fd68692e898e5568725c6d49c527d36a9fb5960ffbdeaa82ff7e",
+ "sha256:f68b3cb8bde357a5d7adc9598d57e22a45dfbea19eb6b98286fa3b288c9cd55c"
],
"markers": "python_version >= '3.10'",
- "version": "==8.26.0"
+ "version": "==8.27.0"
},
"jedi": {
"hashes": [
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index 900119b1..f9ba717e 100755
--- a/docs/CHANGELOG.md
+++ b/docs/CHANGELOG.md
@@ -1,6 +1,29 @@
All notable changes to this project will be documented in this file.
We follow the [Semantic Versioning 2.0.0](http://semver.org/) format.
+## v4.5.9.0 - 2024-09-25 - [PR#1291](https://github.com/NOAA-OWP/inundation-mapping/pull/1291)
+
+Changes Docker base image to `gdal:ubuntu-small` in order to avoid JDK from being carried over in the base image and triggering security vulnerabilities.
+
+This PR incorporates a number of changes to the Docker environment:
+- Changes Docker base image to `gdal:ubuntu-small` in order to avoid JDK from being carried over in the base image and triggering security vulnerabilities. Resolves #1278.
+- Upgrades `fiona` and `jupterlab`. Closes #1270 and closes #1290.
+- Eliminates `whitebox` downloading during `fim_pipeline`. Resolves #1209 and closes #1293.
+
+During testing, it was discovered that many files which are not in the `src` directory, can no longer see the `src\utils` files. Adjusting the dockerfile to add extra values to the PYTHONPATH variable fixed it.
+
+Note: This triggers new docker images to be made.
+
+### Changes
+
+- `Dockerfile`: Changes base image to `gdal:ubuntu-small-3.8.4` and removes code related to JDK
+- `Pipfile` and `Pipfile.lock`: Upgrades `fiona`, `jupyterlab`, and `whitebox`
+- `fim_pre_processing`: Removes `WBT_PATH` assignment
+- `src/`
+ - `agreedem.py` and `unique_pixel_and_allocation.py`: sets `whitebox_dir` to `WBT_PATH`
+
+
+
## v4.5.8.0 - 2024-09-13 - [PR#1165](https://github.com/NOAA-OWP/inundation-mapping/pull/1165)
This PR was originally intended to get Alaska HUCs incorporated into CatFIM, but there were a very, very large array of problems and the tool was unable to run. We have made some major modifications and many more will come in the near future. There are partial hooks and commented code for Alaska integration, but temporarily disabled are included and will be handled by a separate branch / PR.
diff --git a/fim_pre_processing.sh b/fim_pre_processing.sh
index d89c554c..bd556940 100755
--- a/fim_pre_processing.sh
+++ b/fim_pre_processing.sh
@@ -122,7 +122,7 @@ fi
# outputsDir & workDir come from the Dockerfile
outputDestDir=$outputsDir/$runName
tempRunDir=$workDir/$runName
-export WBT_PATH=${tempRunDir}/whitebox_temp
+# export WBT_PATH=${tempRunDir}/whitebox_temp
# default values
if [ "$envFile" = "" ]; then envFile=/$projectDir/config/params_template.env; fi
diff --git a/src/agreedem.py b/src/agreedem.py
index b38c7f35..7384c181 100755
--- a/src/agreedem.py
+++ b/src/agreedem.py
@@ -50,6 +50,7 @@ def agreedem(
# Set wbt envs
wbt = whitebox.WhiteboxTools()
wbt.set_verbose_mode(False)
+ wbt.set_whitebox_dir(os.environ.get("WBT_PATH"))
# ------------------------------------------------------------------
# 1. From Hellweger documentation: Compute the vector grid
diff --git a/src/unique_pixel_and_allocation.py b/src/unique_pixel_and_allocation.py
index e5c71e61..14c3f68f 100755
--- a/src/unique_pixel_and_allocation.py
+++ b/src/unique_pixel_and_allocation.py
@@ -34,6 +34,7 @@ def stream_pixel_zones(stream_pixels, unique_stream_pixels):
# Set wbt envs
wbt = whitebox.WhiteboxTools()
wbt.set_verbose_mode(False)
+ wbt.set_whitebox_dir(os.environ.get("WBT_PATH"))
workspace = os.path.dirname(unique_stream_pixels)
base = os.path.basename(unique_stream_pixels)
diff --git a/tools/aggregate_mannings_calibration.py b/tools/aggregate_mannings_calibration.py
index d447c696..067cd4de 100755
--- a/tools/aggregate_mannings_calibration.py
+++ b/tools/aggregate_mannings_calibration.py
@@ -7,6 +7,8 @@
import pandas as pd
+from utils.shared_functions import compute_stats_from_contingency_table
+
def aggregate_parameter_sets(huc_list_path, calibration_stat_folder, summary_file, mannings_json):
outfolder = os.path.dirname(summary_file)
@@ -70,7 +72,6 @@ def aggregate_parameter_sets(huc_list_path, calibration_stat_folder, summary_fil
mannings_summary_table.to_csv(summary_file, index=False)
## calculate optimal parameter set
- from utils.shared_functions import compute_stats_from_contingency_table
true_positives, true_negatives, false_positives, false_negatives, cell_area, masked_count = (
0,
diff --git a/tools/eval_plots.py b/tools/eval_plots.py
index e534582a..2af666d2 100644
--- a/tools/eval_plots.py
+++ b/tools/eval_plots.py
@@ -4,7 +4,6 @@
import glob
import os
import re
-import sys
from pathlib import Path
import geopandas as gpd
diff --git a/tools/generate_nws_lid.py b/tools/generate_nws_lid.py
index f6a8c77f..f95adfa2 100755
--- a/tools/generate_nws_lid.py
+++ b/tools/generate_nws_lid.py
@@ -2,7 +2,6 @@
import argparse
import os
-import sys
from collections import defaultdict
from pathlib import Path
diff --git a/tools/synthesize_test_cases.py b/tools/synthesize_test_cases.py
index dfe0dac7..ab734bf7 100755
--- a/tools/synthesize_test_cases.py
+++ b/tools/synthesize_test_cases.py
@@ -1,12 +1,10 @@
#!/usr/bin/env python3
import argparse
-import ast
import csv
import json
import os
import re
-import signal
import sys
import traceback
from concurrent.futures import ProcessPoolExecutor, as_completed, wait