cryoem-uoft · nfrasser · Jan 17, 2025 · Jan 14, 2025 · Jan 14, 2025 · Jan 14, 2025
diff --git 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
@@ -117,27 +117,23 @@ 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
 
 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="[email protected]" \
 CRYOSPARC_PASSWORD="password123" \
 jupyter notebook

diff --git a/cryosparc/controllers/job.py b/cryosparc/controllers/job.py
@@ -988,7 +988,7 @@ def print_param_spec(self):
         """
         headings = ["Param", "Title", "Type", "Default"]
         rows = []
-        for key, details in self.full_spec.params:
+        for key, details in self.full_spec.params.items():
             if details.get("hidden") is True:
                 continue
             type = (details["anyOf"][0] if "anyOf" in details else details).get("type", "Any")
@@ -1062,13 +1062,16 @@ def print_output_spec(self):
                                    |             |          | ctf                    | ctf
         """
         specs = self.cs.api.jobs.get_output_specs(self.project_uid, self.uid)
-        headings = ["Output", "Title", "Type", "Result Slots", "Result Types"]
+        headings = ["Output", "Title", "Type", "Result Slots", "Result Types", "Passthrough?"]
         rows = []
         for key, spec in specs.root.items():
+            output = self.model.spec.outputs.root.get(key)
+            if not output:
+                warnings.warn(f"No results for input {key}", stacklevel=2)
+                continue
             name, title, type = key, spec.title, spec.type
-            for slot in spec.slots:
-                slot = as_output_slot(slot)
-                rows.append([name, title, type, slot.name, slot.dtype])
+            for result in output.results:
+                rows.append([name, title, type, result.name, result.dtype, "✓" if result.passthrough else ""])
                 name, title, type = "", "", ""  # only these print once per group
         print_table(headings, rows)
 

diff --git a/cryosparc/tools.py b/cryosparc/tools.py
@@ -26,7 +26,7 @@
 from contextlib import contextmanager
 from functools import cached_property
 from hashlib import sha256
-from io import BytesIO
+from io import BytesIO, TextIOBase
 from pathlib import PurePath, PurePosixPath
 from typing import IO, TYPE_CHECKING, Any, Container, Dict, Iterable, List, Optional, Tuple, Union, get_args
 
@@ -313,7 +313,7 @@ def print_job_types(
         """
         allowed_categories = {category} if isinstance(category, str) else category
         register = self.job_register
-        headings = ["Category", "Job", "Title"]
+        headings = ["Category", "Job", "Title", "Stability"]
         rows = []
         prev_category = None
         for job_spec in register.specs:
@@ -326,7 +326,7 @@ def print_job_types(
 
             category = job_spec.category
             display_category = "" if category == prev_category else category
-            rows.append([display_category, job_spec.type, job_spec.title])
+            rows.append([display_category, job_spec.type, job_spec.title, job_spec.stability])
             prev_category = category
 
         print_table(headings, rows)
@@ -782,13 +782,15 @@ def upload(
             project_uid (str): Project unique ID, e.g., "P3"
             target_path (str | Path): Name or path of file to write in project
                 directory.
-            source (str | bytes | Path | IO | Stream): Local path or file handle to
-                upload. May also specified as raw bytes.
+            source (str | bytes | Path | IO | Stream): Local path or file handle
+                to upload. May also specified as raw bytes.
             overwrite (bool, optional): If True, overwrite existing files.
                 Defaults to False.
         """
         if isinstance(source, bytes):
             source = BytesIO(source)
+        if isinstance(source, TextIOBase):  # e.g., open(p, "r") or StringIO()
+            source = Stream.from_iterator(s.encode() for s in source)
         if not isinstance(source, Stream):
             source = Stream.load(source)
         self.api.projects.upload_file(project_uid, source, path=str(target_path), overwrite=overwrite)

diff --git a/docs/examples/3dflex-custom-latent-trajectory.ipynb b/docs/examples/3dflex-custom-latent-trajectory.ipynb
@@ -608,7 +608,7 @@
     "# so we need to divide the components_mode fields by two to get the total number of components\n",
     "num_components = int(len([x for x in particles.fields() if \"components_mode\" in x]) / 2)\n",
     "\n",
-    "slot_spec = [{\"dtype\": \"components\", \"prefix\": f\"components_mode_{k}\", \"required\": True} for k in range(num_components)]\n",
+    "slot_spec = [{\"dtype\": \"components\", \"name\": f\"components_mode_{k}\"} for k in range(num_components)]\n",
     "job = project.create_external_job(\"W5\", \"Custom Latents\")\n",
     "job.connect(\"particles\", \"J243\", \"particles\", slots=slot_spec)"
    ]

diff --git a/docs/examples/cryolo.ipynb b/docs/examples/cryolo.ipynb
@@ -32,16 +32,14 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Connection succeeded to CryoSPARC command_core at http://cryoem0.sbi:40002\n",
-      "Connection succeeded to CryoSPARC command_vis at http://cryoem0.sbi:40003\n",
-      "Connection succeeded to CryoSPARC command_rtp at http://cryoem0.sbi:40005\n"
+      "Connection succeeded to CryoSPARC API at http://cryoem0.sbi:61002\n"
      ]
     }
    ],
    "source": [
     "from cryosparc.tools import CryoSPARC\n",
     "\n",
-    "cs = CryoSPARC(host=\"cryoem0.sbi\", base_port=40000)\n",
+    "cs = CryoSPARC(host=\"cryoem0.sbi\", base_port=61000)\n",
     "assert cs.test_connection()\n",
     "\n",
     "project = cs.find_project(\"P251\")"
@@ -175,12 +173,12 @@
     "\n",
     "for mic in all_micrographs.rows():\n",
     "    source = mic[\"micrograph_blob/path\"]\n",
-    "    target = job.uid + \"/full_data/\" + source.split(\"/\")[-1]\n",
+    "    target = job.uid + \"/full_data/\"\n",
     "    project.symlink(source, target)\n",
     "\n",
     "for mic in train_micrographs.rows():\n",
     "    source = mic[\"micrograph_blob/path\"]\n",
-    "    target = job.uid + \"/train_image/\" + source.split(\"/\")[-1]\n",
+    "    target = job.uid + \"/train_image/\"\n",
     "    project.symlink(source, target)"
    ]
   },
@@ -293,7 +291,11 @@
     "\n",
     "cryosparc-tools provides a `job.subprocess` function to run arbitrary processes, including `cryolo_*.py` scripts installed in the active conda environment.\n",
     "\n",
-    "Use `job.subprocess` to generate a crYOLO configuration file with the `cryolo_gui.py config` command. Specify a box size of 130 for this dataset."
+    "Use `job.subprocess` to generate a crYOLO configuration file with the `cryolo_gui.py config` command. Specify a box size of 130 for this dataset.\n",
+    "\n",
+    "```{note}\n",
+    "When connecting to a remote CryoSPARC instance, note that `job.subprocess` processes will run on the local machine, not remotely.\n",
+    "```"
    ]
   },
   {
@@ -368,7 +370,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This creates a `cryolo_model.h5` trained model file in the job directory.\n",
+    "Open the External job's \"Events\" tab from CryoSPARC's web interface to view crYOLO's output. When the process completes, crYOLO creates a `cryolo_model.h5` trained model file in the job directory.\n",
     "\n",
     "## Picking\n",
     "\n",