From da6b43c1eb5c087e1fd680f4c05d786d186ab7ce Mon Sep 17 00:00:00 2001
From: Nick Frasser <1693461+nfrasser@users.noreply.github.com>
Date: Tue, 14 Jan 2025 17:52:15 -0500
Subject: [PATCH] docs(tools): README and CHANGELOG update

---
 CHANGELOG.md  |  6 ++++++
 README.md     | 14 +++++---------
 docs/intro.md |  1 -
 3 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 76293caf..e2c39776 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
 ## Next
 
 - BREAKING: replaced low-level `CryoSPARC.cli`, `CryoSPARC.rtp` and `CryoSPARC.vis` attributes with single unified `CryoSPARC.api`
+- BREAKING: When a `job.start()` or `job.run()` is called for an external job, changing the job connections with `job.add_input`, `job.add_output` or `job.connect` will now trigger an error. Please add all inputs and outputs and connect all inputs before running an external job.
 - BREAKING: `CryoSPARC.download_asset(fileid, target)` no longer accepts a directory target. Must specify a filename.
 - BREAKING: removed `CryoSPARC.get_job_specs()`. Use `CryoSPARC.job_register` instead
 - BREAKING: `CryoSPARC.list_assets()` and `Job.list_assets()` return list of models instead of list of dictionaries, accessible with dot-notation
@@ -15,10 +16,15 @@
   - OLD: `cs.get_targets()[0]['hostname']`
   - NEW: `cs.get_targets()[0].hostname`
   - Some top-level target attributes have also been moved into the `.config` attribute
+- BREAKING: `CryoSPARC.print_job_types` `section` argument renamed to `category`
+  - OLD: `cs.print_job_types(section=["extraction", "refinement"])`
+  - NEW: `cs.print_job_types(category=["extraction", "refinement"])`
 - BREAKING: Restructured schema for Job models, many `Job.doc` properties have been internally rearranged
 - Added: `CryoSPARC.job_register` property
 - Added: `job.load_input()` and `job.load_output()` now accept `"default"`, `"passthrough"` and `"all"` keywords for their `slots` argument
 - Added: `job.alloc_output()` now accepts `dtype_params` argument for fields with dynamic shapes
+- Added: `CryoSPARC.print_job_types` now includes a job stability column
+- Added: `Job.print_output_spec` now includes a passthrough indicator column for results
 - Updated: Improved type definitions
 - Deprecated: When adding external inputs and outputs, expanded slot definitions now expect `"name"` key instead of `"prefix"`, support for which will be removed in a future release.
   - OLD: `job.add_input("particle", slots=[{"prefix": "component_mode_1", "dtype": "component", "required": True}])`
diff --git a/README.md b/README.md
index e4c7b3b4..3852404a 100644
--- a/README.md
+++ b/README.md
@@ -117,19 +117,16 @@ rm -rf cryosparc/*.so build dist *.egg-info
 Install dependencies into a new conda environment:
 
 ```sh
-conda create -n cryosparc-tools-example -c conda-forge \
-    python=3 numpy==1.18.5 \
-    pyqt=5 libtiff wxPython=4.1.1 adwaita-icon-theme
+conda create -n cryosparc-tools-example -c conda-forge python=3 numpy=1.18.5 \
+    pyqt=5 libtiff wxPython=4.1.1 adwaita-icon-theme 'setuptools<66'  # exclude these dependencies if you don't need cryolo
 conda activate cryosparc-tools-example
-pip install -U pip
-pip install nvidia-pyindex matplotlib~=3.4.0 pandas==1.1.4 notebook
-pip install "cryolo[c11]"
-pip install -e ".[build]"
+pip install cryosparc-tools matplotlib~=3.4.0 pandas~=1.1.0 notebook
+pip install nvidia-pyindex  # exclude last two steps if you don't need cryolo
+pip install 'cryolo[c11]'
 ```
 
 Run the notebook server with the following environment variables:
 
-- `CRYOSPARC_LICENSE_ID` with Structura-issued CryoSPARC license
 - `CRYOSPARC_EMAIL` with a CryoSPARC user account email
 - `CRYOSPARC_PASSWORD` with a CryoSPARC user account password
 
@@ -137,7 +134,6 @@ You may also need to include `LD_LIBRARY_PATH` which includes the location of
 CUDA Toolkit and cuDNN runtime libraries (e.g., `~/miniconda3/envs/tools/lib/python3.8/site-packages/nvidia/*/lib`).
 
 ```
-CRYOSPARC_LICENSE_ID="xxxxxxxx-xxxx-xxxx-xxxxxxxxxxxx" \
 CRYOSPARC_EMAIL="ali@example.com" \
 CRYOSPARC_PASSWORD="password123" \
 jupyter notebook
diff --git a/docs/intro.md b/docs/intro.md
index 13d3d52d..bee7ba51 100644
--- a/docs/intro.md
+++ b/docs/intro.md
@@ -188,7 +188,6 @@ environment variables. To do the same, define `CRYOSPARC_LICENSE`,
 CryoSPARC license and login credentials:
 
 ```sh
-CRYOSPARC_LICENSE_ID="xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" \
 CRYOSPARC_EMAIL="ali@example.com" \
 CRYOSPARC_PASSWORD="password123" \
 jupyter notebook --no-browser --ip=0.0.0.0 --port=8888