From 16af6b2d0dabb2a98e2373bde779b7ec789d8505 Mon Sep 17 00:00:00 2001 From: hrodmn Date: Sun, 6 Oct 2024 06:00:49 -0500 Subject: [PATCH] use uv, update a few posts --- .github/workflows/publish.yml | 39 +- .gitignore | 2 + _freeze/site_libs/clipboard/clipboard.min.js | 7 - _freeze/site_libs/quarto-listing/list.min.js | 2 - .../quarto-listing/quarto-listing.js | 243 --- about.qmd | 10 +- posts/hls/index.qmd | 32 +- posts/postgrestgis/index.qmd | 4 +- pyproject.toml | 29 + requirements.in | 21 - requirements.txt | 318 --- uv.lock | 1919 +++++++++++++++++ 12 files changed, 1994 insertions(+), 632 deletions(-) delete mode 100644 _freeze/site_libs/clipboard/clipboard.min.js delete mode 100644 _freeze/site_libs/quarto-listing/list.min.js delete mode 100644 _freeze/site_libs/quarto-listing/quarto-listing.js create mode 100644 pyproject.toml delete mode 100644 requirements.in delete mode 100644 requirements.txt create mode 100644 uv.lock diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 4f7d2e1..2336085 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -14,29 +14,27 @@ jobs: cancel-in-progress: true runs-on: ubuntu-latest steps: - - name: Check out repository - uses: actions/checkout@v2 - - - name: Set up Quarto - uses: quarto-dev/quarto-actions/setup@v2 - with: - tinytex: true - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.x' # Version range or exact version of a Python version to use, using SemVer's version range syntax - cache: 'pip' + - uses: actions/checkout@v4 - - name: Set up docker - uses: docker-practice/actions-setup-docker@1.0.11 - timeout-minutes: 12 + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v2 - name: Install system dependencies run: sudo apt update && sudo apt install ghostscript python3-tk + + - name: Install uv + uses: astral-sh/setup-uv@v3 - - name: Install Python packages - run: pip install -r requirements.txt + - name: Set up Python + run: uv python install + + - name: Install the project + run: uv sync --all-extras --dev + + - name: Set up Quarto + uses: quarto-dev/quarto-actions/setup@v2 + with: + tinytex: true - name: Make .netrc env: @@ -55,7 +53,8 @@ jobs: GDAL_DISABLE_READDIR_ON_OPEN: YES GDAL_HTTP_COOKIEJAR: /tmp/cookies.txt GDAL_HTTP_COOKIEFILE: /tmp/cookies.txt - uses: quarto-dev/quarto-actions/render@v2 + run: | + uv run quarto render - name: Publish if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} @@ -63,4 +62,4 @@ jobs: with: target: netlify render: "false" - NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }} \ No newline at end of file + NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }} diff --git a/.gitignore b/.gitignore index bffdab6..c020df6 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,5 @@ /env/ **/.jupyter_cache/** /hidden* +**/.ipynb_checkpoints/** +hrodmn.dev.egg-info/ diff --git a/_freeze/site_libs/clipboard/clipboard.min.js b/_freeze/site_libs/clipboard/clipboard.min.js deleted file mode 100644 index 1103f81..0000000 --- a/_freeze/site_libs/clipboard/clipboard.min.js +++ /dev/null @@ -1,7 +0,0 @@ -/*! 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- if (categoryEl) { - categoryEl.classList.add("active"); - } - - // Filter the listings to this category - filterListingCategory(category); -} - -function filterListingCategory(category) { - const listingIds = Object.keys(window["quarto-listings"]); - for (const listingId of listingIds) { - const list = window["quarto-listings"][listingId]; - if (list) { - if (category === "") { - // resets the filter - list.filter(); - } else { - // filter to this category - list.filter(function (item) { - const itemValues = item.values(); - if (itemValues.categories !== null) { - const categories = itemValues.categories.split(","); - return categories.includes(category); - } else { - return false; - } - }); - } - } - } -} diff --git a/about.qmd b/about.qmd index ae1cf0d..dcd24c2 100644 --- a/about.qmd +++ b/about.qmd @@ -38,10 +38,9 @@ format-links: false ::: {.content-visible when-format="html"} -I am a software engineer at [NCX](https://ncx.com) where I write code to run our -natural capital marketplace. +I am a cloud engineer at [Development Seed](https://developmentseed.org) where I write code to make geospatial data more accessible to all users. My educational background is in forestry and statistics, but I have spent most -of the last decade honing my programming skills on the job at NCX (formerly +of the last decade honing my programming skills on the job at Development Seed and NCX (formerly SilviaTerra). My programming specialty is building clean and elegant systems for processing geospatial data. @@ -50,7 +49,10 @@ geospatial data. ## Experience -**Senior Software Engineer** NCX, Remote | December 2023 - present +**Cloud Engineer** Development Seed | May 2024 - Present + + +**Senior Software Engineer** NCX, Remote | December 2023 - May 2024 * Designed and maintained a network of live applications that serve the NCX platform diff --git a/posts/hls/index.qmd b/posts/hls/index.qmd index 157febd..486262c 100644 --- a/posts/hls/index.qmd +++ b/posts/hls/index.qmd @@ -1,7 +1,7 @@ --- title: "HLS: Your new favorite remote sensing dataset" date: "2/24/2023" -date-modified: "3/20/2023" +date-modified: "10/6/2024" image: "hls.png" fig-cap-location: top keywords: @@ -97,9 +97,11 @@ You can create an account [here](https://urs.earthdata.nasa.gov/). Once your account is active, you will need to add your login credentials to a `.netrc` file in your home directory. You can do this with a single shell command in a Unix system: -```sh + +```{bash} echo "machine urs.earthdata.nasa.gov login password " > ~/.netrc ``` + When GDAL reads the raster data using `curl` it will find your credentials in this file. @@ -109,7 +111,7 @@ to locate and read the raster files correctly. You can choose to include these in a startup script (e.g. `~/.bashrc`) or set them within your Python script: -```sh +```{bash} CPL_VSIL_CURL_USE_HEAD=FALSE GDAL_DISABLE_READDIR_ON_OPEN=YES GDAL_HTTP_COOKIEJAR=/tmp/cookies.txt @@ -146,12 +148,12 @@ catalog = pystac_client.Client.open(CMR_STAC_URL) The HLS data are stored in two separate collections: -* Landsat: `HLSL30.v2.0` +* Landsat: `HLSL30_2.0` -* Sentinel: `HLSS30.v2.0` +* Sentinel: `HLSS30_2.0` ```{python} -HLS_COLLECTION_IDS = ["HLSL30.v2.0", "HLSS30.v2.0"] +HLS_COLLECTION_IDS = ["HLSL30_2.0", "HLSS30_2.0"] ``` There may be good reasons to keep them separate but this difference and one other design choice that we will discuss later make it more tedious to get up @@ -186,14 +188,14 @@ bbox_4326 = transform(transformer_4326.transform, AOI).bounds We can query the STAC catalog for the entire time series by searching the catalog without a `datetime` specification. ```{python} -hls_history_search = catalog.search( - collections=HLS_COLLECTION_IDS, - bbox=bbox_4326, -) - all_items = [] -for page in hls_history_search.pages(): - all_items.extend(page.items) +for collection_id in HLS_COLLECTION_IDS: + hls_history_search = catalog.search( + collections=collection_id, + bbox=bbox_4326, + ) + for page in hls_history_search.pages(): + all_items.extend(page.items) collection_history = { collection: defaultdict(list) for collection in HLS_COLLECTION_IDS @@ -262,7 +264,7 @@ the data without scrambling the bands. ```{python} BAND_CROSSWALK = { - "HLSL30.v2.0": { + "HLSL30_2.0": { "B01": "coastal aerosol", "B02": "blue", "B03": "green", @@ -274,7 +276,7 @@ BAND_CROSSWALK = { "B10": "thermal infrared 1", "B11": "thermal", }, - "HLSS30.v2.0": { + "HLSS30_2.0": { "B01": "coastal aerosol", "B02": "blue", "B03": "green", diff --git a/posts/postgrestgis/index.qmd b/posts/postgrestgis/index.qmd index 2a46642..7591ec6 100644 --- a/posts/postgrestgis/index.qmd +++ b/posts/postgrestgis/index.qmd @@ -142,7 +142,7 @@ Build the docker network: POSTGRES_PASS=password \ POSTGRES_DB=postgrestgis \ POSTGRESTGIS_PORT=25432 \ - docker-compose up -d + docker compose up -d # pause to make sure the docker network gets up and running before we run any # queries @@ -250,7 +250,7 @@ definitely check out the full documentation. ```{python} # | echo: false # | output: false -!docker stop postgrestgis_server_1 postgrestgis_db_1 +!docker compose down ``` diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..d322d64 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,29 @@ +[project] +name = "hrodmn.dev" +version = "0.1.0" +description = "quarto publication with posts about geospatial software" +requires-python = ">=3.11" +dependencies = [ + "click>=8.1.7", + "folium>=0.17.0", + "geojson-pydantic>=1.1.1", + "geopandas>=1.0.1", + "ipykernel>=6.29.5", + "ipython>=8.28.0", + "ipywidgets>=8.1.5", + "jupyter-cache>=1.0.0", + "jupyter-client>=8.6.3", + "matplotlib>=3.9.2", + "odc-stac>=0.3.10", + "pandas>=2.2.3", + "planetary-computer>=1.0.0", + "pre-commit>=4.0.0", + "pyproj>=3.7.0", + "pystac>=1.11.0", + "pystac-client>=0.8.3", + "rasterio>=1.4.1", + "requests>=2.32.3", + "shapely>=2.0.6", + "stackstac>=0.5.1", + "xarray>=2024.9.0", +] diff --git a/requirements.in b/requirements.in deleted file mode 100644 index 83dc060..0000000 --- a/requirements.in +++ /dev/null @@ -1,21 +0,0 @@ -click -folium -geojson_pydantic -geopandas -ipykernel -ipython -ipywidgets -jupyter-cache -jupyter-client -matplotlib -pandas -planetary_computer -pre-commit -pyproj -pystac -pystac_client -rasterio -requests -shapely -stackstac -xarray \ No newline at end of file diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 65cee79..0000000 --- a/requirements.txt +++ /dev/null @@ -1,318 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.10 -# by the following command: -# -# pip-compile --output-file=requirements.txt requirements.in -# -affine==2.4.0 - # via rasterio -asttokens==2.2.1 - # via stack-data -attrs==23.1.0 - # via - # fiona - # jsonschema - # jupyter-cache - # rasterio -backcall==0.2.0 - # via ipython -branca==0.6.0 - # via folium -certifi==2022.12.7 - # via - # fiona - # pyproj - # rasterio - # requests -cfgv==3.3.1 - # via pre-commit -charset-normalizer==3.1.0 - # via requests -click==8.1.3 - # via - # -r requirements.in - # click-plugins - # cligj - # dask - # fiona - # jupyter-cache - # planetary-computer - # rasterio -click-plugins==1.1.1 - # via - # fiona - # rasterio -cligj==0.7.2 - # via - # fiona - # rasterio -cloudpickle==2.2.1 - # via dask -comm==0.1.3 - # via ipykernel -contourpy==1.0.7 - # via matplotlib -cycler==0.11.0 - # via matplotlib -dask[array]==2023.4.1 - # via stackstac -debugpy==1.6.7 - # via ipykernel -decorator==5.1.1 - # via ipython -distlib==0.3.6 - # via virtualenv -executing==1.2.0 - # via stack-data -fastjsonschema==2.16.3 - # via nbformat -filelock==3.12.0 - # via virtualenv -fiona==1.9.3 - # via geopandas -folium==0.14.0 - # via -r requirements.in -fonttools==4.39.3 - # via matplotlib -fsspec==2023.4.0 - # via dask -geojson-pydantic==0.5.0 - # via -r requirements.in -geopandas==0.12.2 - # via -r requirements.in -greenlet==2.0.2 - # via sqlalchemy -identify==2.5.24 - # via pre-commit -idna==3.4 - # via requests -importlib-metadata==6.6.0 - # via - # dask - # jupyter-cache -ipykernel==6.22.0 - # via - # -r requirements.in - # ipywidgets -ipython==8.13.1 - # via - # -r requirements.in - # ipykernel - # ipywidgets -ipywidgets==8.0.6 - # via -r requirements.in -jedi==0.18.2 - # via ipython -jinja2==3.1.2 - # via - # branca - # folium -jsonschema==4.17.3 - # via nbformat -jupyter-cache==0.6.1 - # via -r requirements.in -jupyter-client==8.0.3 - # via - # -r requirements.in - # ipykernel - # nbclient -jupyter-core==5.3.0 - # via - # ipykernel - # jupyter-client - # nbclient - # nbformat -jupyterlab-widgets==3.0.7 - # via ipywidgets -kiwisolver==1.4.4 - # via matplotlib -locket==1.0.0 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planetary-computer - # pystac-client -shapely==2.0.1 - # via - # -r requirements.in - # geopandas -six==1.16.0 - # via - # asttokens - # munch - # python-dateutil -snuggs==1.4.7 - # via rasterio -sqlalchemy==2.0.12 - # via jupyter-cache -stack-data==0.6.2 - # via ipython -stackstac==0.4.3 - # via -r requirements.in -tabulate==0.9.0 - # via jupyter-cache -toolz==0.12.0 - # via - # dask - # partd -tornado==6.3.1 - # via - # ipykernel - # jupyter-client -traitlets==5.9.0 - # via - # comm - # ipykernel - # ipython - # ipywidgets - # jupyter-client - # jupyter-core - # matplotlib-inline - # nbclient - # nbformat -typing-extensions==4.5.0 - # via - # pydantic - # sqlalchemy -tzdata==2023.3 - # via pandas -urllib3==1.26.15 - # via requests -virtualenv==20.23.0 - # via pre-commit -wcwidth==0.2.6 - # via prompt-toolkit -widgetsnbextension==4.0.7 - # via ipywidgets -xarray==2023.4.2 - # via - # -r requirements.in - # stackstac -zipp==3.15.0 - # via importlib-metadata - -# The following packages 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