cloudos-cli 2.90.2__tar.gz → 2.92.0__tar.gz

{cloudos_cli-2.90.2 → cloudos_cli-2.92.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.90.2
+Version: 2.92.0
 Summary: Python package for interacting with the Lifebit Platform
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -109,11 +109,11 @@ Python package for interacting with Lifebit Platform
       - [Move Files](#move-files)
       - [Rename Files](#rename-files)
       - [Copy Files](#copy-files)
-      - [Link S3 Folders to Interactive Analysis](#link-s3-folders-to-interactive-analysis)
+      - [Link Files and Folders to Interactive Analysis](#link-files-and-folders-to-interactive-analysis)
       - [Create Folder](#create-folder)
       - [Remove Files or Folders](#remove-files-or-folders)
     - [Link](#link)
-      - [Link Folders to Interactive Analysis](#link-folders-to-interactive-analysis)
+      - [Link Files and Folders to Interactive Analysis](#link-files-and-folders-to-interactive-analysis-1)
     - [Procurement](#procurement)
       - [List Procurement Images](#list-procurement-images)
       - [Set Procurement Organization Image](#set-procurement-organization-image)
@@ -231,10 +231,10 @@ This will tell you the implemented commands. Each implemented command has its ow
 ```bash
 cloudos job list --help
 ```
-```console                                                                                                      Usage: cloudos job list [OPTIONS]                                                                          
-                                                                                                            
- Collect workspace jobs from a Lifebit Platform workspace in CSV or JSON format.                                     
-                                                                                                            
+```console                                                                                                      Usage: cloudos job list [OPTIONS]
+
+ Collect workspace jobs from a Lifebit Platform workspace in CSV or JSON format.
+
 ╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────╮
 │ *  --apikey                    -k  TEXT        Your Lifebit Platform API key [required]                           │
 │ *  --cloudos-url               -c  TEXT        The Lifebit Platform url you are trying to access to.              │
@@ -299,7 +299,7 @@ $HOME
 
 ### Configure Default Profile
 
-To facilitate the reuse of required parameters, you can create profiles. 
+To facilitate the reuse of required parameters, you can create profiles.
 
 To generate a profile called `default`, use the following command:
 
@@ -321,7 +321,7 @@ The same prompts will appear, including the execution platform (aws or azure). I
 
 When configuring a profile, you can specify:
 - **API Key**: Your Lifebit Platform API credentials
-- **Platform URL**: The Lifebit Platform instance URL  
+- **Platform URL**: The Lifebit Platform instance URL
 - **Project Name**: Default project for commands
 - **Execution Platform**: `aws` (default) or `azure` - determines default instance types and available features
 - **Repository Platform**: Version control system (github, gitlab, etc.)
@@ -1314,7 +1314,7 @@ cloudos job cost --profile my_profile --job-id 62c83a1191fe06013b7ef355
 The expected output is a formatted table showing:
 
 ```console
-                              Job Cost Details - Job ID: 62c83a1191fe06013b7ef355                              
+                              Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
 ┏━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┓
 ┃        ┃            ┃            ┃            ┃          ┃             ┃            ┃ Compute     ┃         ┃
 ┃        ┃ Instance   ┃            ┃ Life-cycle ┃          ┃ Compute     ┃ Instance   ┃ storage     ┃         ┃
@@ -1343,7 +1343,7 @@ On page 1/2: n = next, p = prev, q = quit
 
 By pressing 'n', it will show the next page or the last if it is the case.
 
-                              Job Cost Details - Job ID: 62c83a1191fe06013b7ef355                              
+                              Job Cost Details - Job ID: 62c83a1191fe06013b7ef355
 ┏━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┓
 ┃        ┃            ┃            ┃            ┃          ┃             ┃            ┃ Compute     ┃         ┃
 ┃        ┃ Instance   ┃            ┃ Life-cycle ┃          ┃ Compute     ┃ Instance   ┃ storage     ┃         ┃
@@ -1462,7 +1462,7 @@ The expected output is a formatted table showing:
 ```console
 Total related analyses found: 15
 
-                                              Related Analyses                                              
+                                              Related Analyses
 ┏━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┳━━━━━━━━━━━━┓
 ┃ Status    ┃ Name                               ┃ Owner          ┃ ID                       ┃ Submit time         ┃ Run time  ┃ Total Cost ┃
 ┡━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━╇━━━━━━━━━━━━┩
@@ -1944,7 +1944,7 @@ Example Python Script:
 #!/usr/bin/python3
 print("Hello world")
 ```
- 
+
 2. Or use an interpreter command in the executable field
 
 If your script doesn’t have a shebang line, you can execute it by explicitly specifying the interpreter in the executable command:
@@ -2021,7 +2021,7 @@ Interactive sessions allow you to work within the platform using different virtu
 
 You can get a list of all interactive sessions in your workspace by running `cloudos interactive-session list`. The command can produce three different output formats that can be selected using the `--output-format` option:
 
-- **stdout** (default): Displays a table directly in the terminal with interactive pagination 
+- **stdout** (default): Displays a table directly in the terminal with interactive pagination
 - **csv**: Saves session data to a CSV file with a minimum predefined set of columns by default, or all available columns using the `--all-fields` parameter
 - **json**: Saves complete session information to a JSON file with all available fields
 
@@ -2036,7 +2036,7 @@ cloudos interactive-session list --profile my_profile --output-format stdout
 The table displays sessions with pagination controls (press `n` for next page, `p` for previous page, or `q` to quit):
 
 ```console
-                          Interactive Sessions                          
+                          Interactive Sessions
 ┏━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━┓
 ┃ Status  ┃ Name         ┃ Type           ┃ ID            ┃ Owner  ┃
 ┡━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━┩
@@ -2183,7 +2183,7 @@ cloudos interactive-session create \
 
 **Data & Storage Management:**
 - `--mount`: Mount a data file into the session. Supports both Lifebit Platform datasets and S3 files (AWS only). Format: `project_name/dataset_path` (e.g., `leila-test/Data/file.csv`) or `s3://bucket/path/to/file` (e.g., `s3://my-bucket/data/file.csv`). Can be used multiple times.
-- `--link`: Link a folder into the session for read/write access (AWS only). Supports S3 folders (e.g., `s3://my-bucket/data/`) and File Explorer folders (e.g., `my-project/Data/results`). Multiple folders can be specified using multiple `--link` flags or as comma-separated paths in a single `--link` argument. 
+- `--link`: Link a file or folder into the session for read access (AWS only). Supports S3 files/folders (e.g., `s3://my-bucket/data/file.csv`, `s3://my-bucket/data/`) and File Explorer files/folders (e.g., `my-project/Data/file.csv`, `my-project/Data/results`). S3 paths whose last segment contains a `.` are treated as files; paths ending with `/` or without an extension are treated as folders. Multiple items can be specified using multiple `--link` flags or as comma-separated paths in a single `--link` argument.
 **Note:** Linking is not supported on Azure. Use Lifebit Platform File Explorer for data access.
 
 **Backend-Specific:**
@@ -2198,7 +2198,7 @@ cloudos interactive-session create \
 
 CloudOS CLI supports multiple ways to access data in interactive sessions, depending on your execution platform:
 - **Mount files** (`--mount`): Files are copied into the session's mounted-data volume. Supports CloudOS File Explorer files and S3 files (AWS only).
-- **Link folders** (`--link`): Folders are mounted as read/write accessible directories in the session (AWS only). Supports both S3 folders and Lifebit Platform File Explorer folders. Linked folders appear with unique mount names based on the folder path. 
+- **Link files/folders** (`--link`): Files and folders are mounted as read-accessible items in the session (AWS only). Supports S3 files, S3 folders, and Lifebit Platform File Explorer files and folders. Linked items appear with unique mount names based on the item name. Maximum 100 items per session.
 
 
 **Data Mounting Examples**
@@ -2572,7 +2572,7 @@ The command automatically loads from profile (via `@with_profile_config` decorat
 
 #### Resume Interactive Session
 
-Resume a paused interactive session with optional configuration updates. You can change instance type, storage, cost limit, auto-shutdown time, and mount additional data files or folders when resuming.
+Resume a paused interactive session with optional configuration updates. You can change instance type, storage, cost limit, and auto-shutdown time when resuming.
 
 
 **Basic Usage**
@@ -2604,19 +2604,6 @@ cloudos interactive-session resume \
   --shutdown-in 12h
 ```
 
-**Mount Additional Data**
-
-Resume and mount additional files:
-
-```bash
-cloudos interactive-session resume \
-  --session-id <SESSION_ID> \
-  --profile my_profile \
-  --mount my-project/Data/new-dataset.csv \
-  --mount s3://my-bucket/data/file.txt
-```
-
-
 **Configuration Updates**
 
 All configuration parameters are optional. If not specified, the session resumes with its previous configuration.
@@ -2626,6 +2613,8 @@ All configuration parameters are optional. If not specified, the session resumes
 - `--cost-limit <USD>` - Update compute cost limit (-1 for unlimited)
 - `--shutdown-in <DURATION>` - Update auto-shutdown time (e.g., 8h, 2d)
 
+> To link or mount data to a running session, use `cloudos link` or `cloudos datasets link` after the session has resumed.
+
 ### Datasets
 
 Manage files and folders within your Lifebit Platform File Explorer programmatically. These commands provide comprehensive file management capabilities for organizing research data and results.
@@ -2657,7 +2646,7 @@ The `datasets ls` command supports different output formats using the `--output-
 - **`stdout` (default)**: Displays results in the console with Rich formatting
   - Without `--details`: Simple list of file/folder names with color coding (blue underlined for folders)
   - With `--details`: Rich formatted table with all file information
-  
+
 - **`csv`**: Saves results to a CSV file
   - Without `--details`: CSV with two columns: "Name,Storage Path"
   - With `--details`: CSV with columns "Type, Owner, Size, Size (bytes), Last Updated, Virtual Name, Storage Path"
@@ -2707,7 +2696,7 @@ Any of the `source_path` must be a full path, starting from the `Data` datasets
 An example of such command is:
 
 ```
-cloudos datasets mv Data/results/my_plot.png Data/plots 
+cloudos datasets mv Data/results/my_plot.png Data/plots
 ```
 
 #### Rename Files
@@ -2718,7 +2707,7 @@ Change file and folder names while keeping them in the same location. This helps
 > Files and folders within the `Data` dataset can be renamed using the following command
 
 ```bash
-cloudos datasets rename <path> <new_name> --profile my_profile 
+cloudos datasets rename <path> <new_name> --profile my_profile
 ```
 where `path` is the full path to the file/folder to be renamed and `new_name` is just the name, no path required, as the file will not be moved.
 
@@ -2744,40 +2733,53 @@ or it can happen **across different projects**  within the same workspace
 cloudos datasets cp <source_path> <destination_path> --profile <profile> --destination-project-name <project>
 ```
 
-Any of the `source_path` must be a full path; any `destination_path` must be a path starting with `Data` and finishing with the folder where to move the file/folder. 
+Any of the `source_path` must be a full path; any `destination_path` must be a path starting with `Data` and finishing with the folder where to move the file/folder.
 
 An example of such command is:
 
 ```
-cloudos datasets cp AnalysesResults/my_analysis/results/my_plot.png Data/plots 
+cloudos datasets cp AnalysesResults/my_analysis/results/my_plot.png Data/plots
 ```
 
 
-#### Link S3 Folders to Interactive Analysis
+#### Link Files and Folders to Interactive Analysis
 
-Connect external S3 buckets or internal File Explorer folders to your interactive analysis sessions. This provides direct access to data without needing to copy files.
+Connect external S3 buckets, S3 files, or File Explorer files/folders to your interactive analysis sessions. This provides direct access to data without needing to copy files.
 
-This subcommand is using the option `--session-id` to access the correct interactive session. This option can be added to the CLI or defined in a profile, for convenience.
+This subcommand uses the `--session-id` option to access the correct interactive session. This option can be added to the CLI or defined in a profile, for convenience.
 
 ```bash
-cloudos datasets link <S3_FOLDER_COMPLETE_PATH_OR_VIRTUAL_FOLDER_PATH> --profile <profile> --session-id <SESSION_ID>
+cloudos datasets link <PATH> --profile <profile> --session-id <SESSION_ID>
 ```
 
-For example, an s3 folder can be linked like follows
+Link an S3 folder:
 ```console
 cloudos datasets link s3://bucket/path/folder --profile test --session-id 1234
 ```
 
-A virtual folder can be linked like
-``` concole
-cloudos datasets link "Analyses Results/HLA" --session-id 1234
+Link an S3 file:
+```console
+cloudos datasets link s3://bucket/path/data.csv --profile test --session-id 1234
+```
+
+Link a File Explorer folder (requires `--project-name`):
+```console
+cloudos datasets link "Data/HLA" --project-name my-project --session-id 1234
+```
+
+Link a File Explorer file (requires `--project-name`):
+```console
+cloudos datasets link "Data/observations.csv" --project-name my-project --session-id 1234
 ```
 
 > [!NOTE]
 > If running the CLI inside a jupyter session, the pre-configured CLI installation will have the session ID already installed and only the `--apikey` needs to be added.
 
 > [!NOTE]
-> Virtual folders in File Explorer, the ones a user has created in File explorer and are not actual storage locations, cannot be linked.
+> Virtual folders in File Explorer (folders created in File Explorer that are not actual storage locations) cannot be linked.
+
+> [!NOTE]
+> A maximum of 100 items can be linked per session. If the new items combined with already-linked items exceed this limit, the entire request is rejected.
 
 #### Create Folder
 
@@ -2787,7 +2789,7 @@ Create new organizational folders within your projects to maintain structured da
 > New folders can be created within the `Data` dataset and its subfolders.
 
 ```bash
-cloudos datasets mkdir <new_folder_path> --profile my_profile 
+cloudos datasets mkdir <new_folder_path> --profile my_profile
 ```
 
 #### Remove Files or Folders
@@ -2795,23 +2797,23 @@ cloudos datasets mkdir <new_folder_path> --profile my_profile
 Remove unnecessary files or empty folders from your File Explorer. Note that this removes files from Lifebit Platform but not from underlying cloud storage.
 
 > [!NOTE]
-> Files and folders can be removed in the `Data` datasets and its subfolders. 
+> Files and folders can be removed in the `Data` datasets and its subfolders.
 
 ```bash
 cloudos datasets rm <path> --profile my_profile
 ```
 > [!NOTE]
 > If a file was uploaded by the user, in order to be removed you must use  `--force` and that will permanently remove the file. If the file is "linked" (e.g a s3 folder or file), removing it using `cloudos datasets rm` will not remove it from the the s3 bucket.
- 
+
 ---
 
 ### Link
 
-The `cloudos link` command provides a unified interface for linking folders to interactive analysis sessions. This command consolidates functionality previously available through separate commands (`cloudos job results --link`, `cloudos job workdir --link`, `cloudos job logs --link`, and `cloudos datasets link`) into a single, intuitive interface.
+The `cloudos link` command provides a unified interface for linking files and folders to interactive analysis sessions. This command consolidates functionality previously available through separate commands (`cloudos job results --link`, `cloudos job workdir --link`, `cloudos job logs --link`, and `cloudos datasets link`) into a single, intuitive interface.
 
-#### Link Folders to Interactive Analysis
+#### Link Files and Folders to Interactive Analysis
 
-Link job-related folders or custom S3 paths to your interactive analysis sessions for direct access to data without needing to copy files.
+Link job-related folders or custom S3/File Explorer paths (files and folders) to your interactive analysis sessions for direct access to data without needing to copy files.
 
 **Two modes of operation:**
 
@@ -2819,8 +2821,10 @@ Link job-related folders or custom S3 paths to your interactive analysis session
    - By default, links results, workdir, and logs folders
    - Use `--results`, `--workdir`, or `--logs` flags to link only specific folders
 
-2. **Direct path linking** (PATH argument): Links specific S3 or File Explorer paths. It supports a single path or comma-separated multiple paths.
-   
+2. **Direct path linking** (PATH argument): Links specific S3 or File Explorer paths (files or folders). Supports a single path or comma-separated multiple paths.
+   - S3 paths whose last segment contains a `.` are treated as files (e.g., `s3://bucket/data/file.csv`)
+   - S3 paths ending with `/` or without an extension are treated as folders
+   - File Explorer paths can point to either files or folders — the CLI detects the type automatically
 
 **Basic usage:**
 
@@ -2832,16 +2836,28 @@ cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --profile my_profile
 cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --results --profile my_profile
 cloudos link --job-id <JOB_ID> --session-id <SESSION_ID> --workdir --logs --profile my_profile
 
-# Link a single S3 path
-cloudos link s3://bucket/folder --session-id <SESSION_ID> --profile my_profile
+# Link a single S3 folder
+cloudos link s3://bucket/folder/ --session-id <SESSION_ID> --profile my_profile
 
-# Link multiple S3 paths (comma-separated)
-cloudos link s3://bucket1/data,s3://bucket2/results,s3://bucket3/output --session-id <SESSION_ID> --profile my_profile
+# Link a single S3 file
+cloudos link s3://bucket/data/file.csv --session-id <SESSION_ID> --profile my_profile
 
-# Link a File Explorer path (requires project name)
+# Link multiple S3 paths (comma-separated, files and folders mixed)
+cloudos link s3://bucket1/data/,s3://bucket2/results/file.csv --session-id <SESSION_ID> --profile my_profile
+
+# Link a File Explorer folder (path is RELATIVE to --project-name; do NOT prepend the project)
 cloudos link "Data/MyFolder" --project-name my-project --session-id <SESSION_ID> --profile my_profile
+
+# Link a File Explorer file (path is RELATIVE to --project-name)
+cloudos link "Data/file.csv" --project-name my-project --session-id <SESSION_ID> --profile my_profile
+
+# Link several File Explorer items at once (all in the same project)
+cloudos link "Data/MyFolder,Data/file.csv,Results/run-1" --project-name my-project --session-id <SESSION_ID> --profile my_profile
 ```
 
+> [!IMPORTANT]
+> **`cloudos link` is single-project for File Explorer paths.** All File Explorer items linked in one invocation must belong to the project named in `--project-name`. The path must be relative to that project — prepending the project name to the path (e.g. `my-project/Data/file.csv`) is rejected. To link items from a different project, run `cloudos link` again with a different `--project-name`.
+
 **Command options:**
 
 
@@ -2851,7 +2867,7 @@ cloudos link "Data/MyFolder" --project-name my-project --session-id <SESSION_ID>
 - `--workspace-id`: The specific Lifebit Platform workspace ID (required)
 - `--session-id`: The specific Lifebit Platform interactive session ID (required)
 - `--job-id`: The job ID in Lifebit Platform (links results, workdir, and logs by default)
-- `--project-name`: Lifebit Platform project name (required for File Explorer paths)
+- `--project-name`: Lifebit Platform project name. Required when any PATH is a File Explorer path. All FE paths in one invocation must belong to this project and must be RELATIVE to it (do not prepend the project name)
 - `--results`: Link only results folder (only works with `--job-id`)
 - `--workdir`: Link only working directory (only works with `--job-id`)
 - `--logs`: Link only logs folder (only works with `--job-id`)
@@ -2910,7 +2926,7 @@ To list images for a specific procurement, use the following command:
 
 ```bash
 cloudos procurement images ls \
-    -- profile procurement_profile 
+    -- profile procurement_profile
     --procurement-id "your_procurement_id_here"
 ```
 
@@ -2969,12 +2985,10 @@ cloudos procurement images set --profile procurement_profile --image-type "JobDe
 - `--image-type`: The Lifebit Platform resource image type (required). Possible values:
   - `RegularInteractiveSessions`
   - `SparkInteractiveSessions`
-  - `RStudioInteractiveSessions`
-  - `JupyterInteractiveSessions`
   - `JobDefault`
   - `NextflowBatchComputeEnvironment`
-- `--provider`: The cloud provider (required). Currently only `aws` is supported
-- `--region`: The cloud region (required). Currently only AWS regions are supported
+- `--provider`: The cloud provider (required). Currently only supporting `aws` and `azure`.
+- `--region`: The cloud region (required). Currently only supporting aws and azure regions.
 - `--image-id`: The new image ID value (required)
 - `--image-name`: The new image name value (optional)
 - `--image-version`: The new image version (required)
@@ -3007,7 +3021,7 @@ cloudos procurement images reset --profile procurement_profile --image-type "Job
 - `--organisation-id`: The organization ID where the change will be applied (required)
 - `--image-type`: The Lifebit Platform resource image type (required). Same values as for `set` command
 - `--provider`: The cloud provider (required). Currently only `aws` is supported
-- `--region`: The cloud region (required). Currently only AWS regions are supported
+- `--region`: The cloud region (required). Currently only supporting aws and azure regions.
 - `--disable-ssl-verification`: Disable SSL certificate verification
 - `--ssl-cert`: Path to your SSL certificate file
 - `--profile`: Profile to use from the config file
@@ -3036,7 +3050,7 @@ Executing status...
 	Current Cromwell server status is: Stopped
 ```
 
-```bash    
+```bash
 # Cromwell start
 cloudos cromwell start --profile my_profile
 ```
@@ -3262,8 +3276,8 @@ responses>=0.21.0
 mock>=3.0.5
 ```
 
-Command to run tests from the `cloudos-cli` main folder: 
+Command to run tests from the `cloudos-cli` main folder:
 
 ```
 python -m pytest -s -v
-``` 
+```