Release 0.7.0 (#68)

.markdownlint.yaml

@@ -1,3 +1,6 @@
 default: true
-MD024: # no-duplicate-heading/no-duplicate-header
-  allow_different_nesting: true
+no-duplicate-heading:
+  # Check for duplicate headings only amongst sibling headings.  Allow duplicate
+  # headings in separate sections, which is common in CHANGELOGs (e.g., Fixed,
+  # Added, Changed).
+  siblings_only: true

CHANGELOG.md

@@ -7,6 +7,8 @@ The format is based on [Keep a Changelog], and this project adheres to
 
 ## Unreleased
 
+### 0.7.0 (2024-04-23)
+
 ### Added
 
 - [#57](https://github.com/MAAP-Project/gedi-subsetter/issues/57) Users may
@@ -16,10 +18,10 @@ The format is based on [Keep a Changelog], and this project adheres to
   download failures are now retried up to 10 times to reduce the likelihood that
   subsetting will fail due to a download failure.
 - [#56](https://github.com/MAAP-Project/gedi-subsetter/issues/56) The
-  `bin/subset` script now captures output to `stderr` and writes it to the log
-  file named `gedi-subset.log`.  When a job succeeds, the log file will appear
-  in the job's output directory.  Otherwise, it will appear in the jobs triage
-  directory.
+  `bin/subset.sh` script now captures output to `stderr` and writes it to the
+  log file named `gedi-subset.log`.  When a job succeeds, the log file will
+  appear in the job's output directory.  Otherwise, it will appear in the job's
+  triage directory.
 - [#65](https://github.com/MAAP-Project/gedi-subsetter/issues/65) All supported
   GEDI collections are now cloud-hosted, and granules are now downloaded from
   the cloud rather than from DAAC servers.

algorithm_config.yaml

@@ -1,12 +1,12 @@
 algorithm_description: Subset GEDI L1B, L2A, L2B, or L4A granules within an area of interest (AOI)
 algorithm_name: gedi-subset
-algorithm_version: 0.6.2
+algorithm_version: 0.7.0
 repository_url: https://github.com/MAAP-Project/gedi-subsetter.git
-docker_container_url: mas.maap-project.org/root/maap-workspaces/base_images/vanilla:v3.1.4
+docker_container_url: mas.maap-project.org/root/maap-workspaces/base_images/vanilla:v3.1.5
 disk_space: 20GB
 queue: maap-dps-worker-32gb
 build_command: gedi-subsetter/bin/build-dps
-run_command: gedi-subsetter/bin/subset
+run_command: gedi-subsetter/bin/subset.sh
 inputs:
   config: []
   file:

bin/install

@@ -31,7 +31,7 @@ done
 # PIP_REQUIRE_VENV=0 to avoid complaints about installing packages outside of a
 # virtual environment.
 PIP_REQUIRE_VENV=0 "${run}" conda lock install "${conda_lock_args[@]}" \
-    --name "${conda_env_name}"
+    --name "${conda_env_name}" "${basedir}/conda-lock.yml"
 
 # pip install gedi-subsetter in editable mode.
 PIP_REQUIRE_VENV=0 "${run}" python -m pip install -e "${basedir}" --no-deps

bin/run

@@ -27,6 +27,13 @@ if ! "${conda}" env list | grep -q gedi_subset; then
     exit 1
 fi
 
+# We must set the MAAP_CONF environment variable to point to the preinstalled
+# maap-py package.  This is necessary because MAAP_CONF is no longer set
+# automatically in the Docker container (as it was in the past), and the changes
+# I had previously made to maap-py to read maap.cfg as a bundled resource file
+# were reverted.
+export MAAP_CONF=/maap-py/
+
 [[ -n "${quiet}" ]] || set -x
 
 if [[ "${CI:-}" == "true" ]]; then

bin/subset → bin/subset.sh

@@ -2,9 +2,9 @@
 
 set -euo pipefail
 
-# Apply dirname twice to get to the top of the repo, since this script is in the
-# `bin` directory (i.e., first dirname gets to `bin`, second gets to the top).
-base_dir=$(dirname "$(dirname "$(readlink -f "$0")")")
+bin=$(dirname "$(readlink -f "$0")")
+base_dir=$(dirname "${bin}")
+run="${bin}/run"
 
 input_dir="${PWD}/input"
 output_dir="${PWD}/output"
@@ -18,6 +18,10 @@ if ! test -d "${input_dir}"; then
     # within it.
     command=("${subset_py}" --verbose "$@")
 else
+    echo "--- >>> ${input_dir} ---" >&2
+    ls -l "${input_dir}" >&2
+    echo "--- <<< ${input_dir} ---" >&2
+
     # There is an `input` sub-directory of the current working directory, so
     # assume the AOI file is the sole file within the `input` sub-directory.
     aoi="$(ls "${input_dir}"/*)"
@@ -72,7 +76,8 @@ mkdir -p "${output_dir}"
 # to write directly to a file because it is a tricky feat to coordinate logging
 # from multiple processes into a single file.
 logfile="${PWD}/gedi-subset.log"
-"${CONDA_EXE:-conda}" run --no-capture-output --name gedi_subset "${command[@]}" 2>"${logfile}"
+
+"${run}" "${command[@]}" 2>"${logfile}"
 
 # If we get here, the command above succeeded (otherwise this script would have
 # exited with a non-zero status).  We can now move the log file to the output