CLI installation and updating

.claude-plugin/marketplace.json

@@ -11,7 +11,7 @@
       "name": "asta",
       "source": "./plugins/asta",
       "description": "Paper search, metadata, and document management for scientific research",
-      "version": "0.8.0",
+      "version": "0.8.1",
       "author": {
         "name": "AI2 Asta Team"
       },
@@ -29,7 +29,7 @@
       "name": "asta-preview",
       "source": "./plugins/asta-preview",
       "description": "Paper search, metadata, document management, literature reports, and experiments for scientific research",
-      "version": "0.8.0",
+      "version": "0.8.1",
       "author": {
         "name": "AI2 Asta Team"
       },

DEVELOPER.md

@@ -494,7 +494,7 @@ make version
 ```bash
 make set-version VERSION=x.y.z
 ```
-- Updates `__init__.py`, `pyproject.toml`, and `marketplace.json`
+- Updates all locations where version is referenced
 - Run `make build-plugins` after to regenerate plugin packages
 - Fails with error if VERSION parameter is not provided
 - Provides suggested commit command after success

Makefile

@@ -104,43 +104,21 @@ publish-test: build
 
 # Set version in all files
 set-version:
-	@if [ -z "$(VERSION)" ]; then \
-		echo "Error: VERSION parameter is required. Usage: make set-version VERSION=x.y.z"; \
-		exit 1; \
-	fi; \
-	echo "Setting version to $(VERSION) in all files..."; \
-	echo "Updating src/asta/__init__.py..."; \
-	sed -i.bak 's/__version__ = ".*"/__version__ = "$(VERSION)"/' src/asta/__init__.py && rm src/asta/__init__.py.bak; \
-	echo "Updating pyproject.toml..."; \
-	sed -i.bak 's/^version = ".*"/version = "$(VERSION)"/' pyproject.toml && rm pyproject.toml.bak; \
-	echo "Updating .claude-plugin/marketplace.json..."; \
-	uv run python -c "import json; f = open('.claude-plugin/marketplace.json', 'r'); data = json.load(f); f.close(); [p.__setitem__('version', '$(VERSION)') for p in data['plugins']]; f = open('.claude-plugin/marketplace.json', 'w'); json.dump(data, f, indent=2); f.write('\n'); f.close()"; \
-	echo "Version set to $(VERSION)"; \
-	echo "Now run: make build-plugins"
+	@uv run python scripts/manage-version.py set $(VERSION)
 
 # Create and push git tag using version from code
 push-version-tag:
-	@echo "Checking version consistency..."; \
-	INIT_VERSION=$$(uv run python -c "from src.asta import __version__; print(__version__)"); \
-	PYPROJECT_VERSION=$$(grep '^version = ' pyproject.toml | sed 's/version = "\(.*\)"/\1/'); \
-	MARKETPLACE_VERSION=$$(uv run python -c "import json; data = json.load(open('.claude-plugin/marketplace.json')); print(data['plugins'][0]['version'])"); \
-	if [ "$$INIT_VERSION" != "$$PYPROJECT_VERSION" ] || [ "$$INIT_VERSION" != "$$MARKETPLACE_VERSION" ]; then \
-		echo "Error: Version mismatch detected:"; \
-		echo "  src/asta/__init__.py:            $$INIT_VERSION"; \
-		echo "  pyproject.toml:                  $$PYPROJECT_VERSION"; \
-		echo "  .claude-plugin/marketplace.json: $$MARKETPLACE_VERSION"; \
-		echo ""; \
-		echo "Run 'make set-version VERSION=x.y.z' to sync versions"; \
+	@if ! uv run python scripts/manage-version.py check; then \
 		exit 1; \
 	fi; \
-	VERSION=$$INIT_VERSION; \
+	VERSION=$$(uv run python scripts/manage-version.py show); \
 	git tag v$$VERSION && \
 	git push origin v$$VERSION && \
 	echo "Pushed tag v$$VERSION"
 
 # Show current version
 version:
-	@uv run python -c "from src.asta import __version__; print(__version__)"
+	@uv run python scripts/manage-version.py show
 
 # Quick check before commit
 check: format-check lint test-unit

hooks/hooks.json

@@ -7,6 +7,10 @@
           {
             "type": "command",
             "command": "mkdir -p ~/.asta/literature"
+          },
+          {
+            "type": "command",
+            "command": "bash ${CLAUDE_PLUGIN_ROOT}/hooks/sync-cli-version.sh"
           }
         ]
       }

hooks/sync-cli-version.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+# Check if asta CLI version matches the plugin version and auto-install/update if needed
+
+PLUGIN_VERSION=0.8.1
+INSTALL_URL="git+https://github.com/allenai/asta-plugins.git@v$PLUGIN_VERSION"
+
+# Check if asta is installed
+if ! command -v asta &> /dev/null; then
+    echo "📦 Installing Asta CLI version $PLUGIN_VERSION..."
+    if uv tool install "$INSTALL_URL"; then
+        echo "✅ Asta CLI $PLUGIN_VERSION installed successfully"
+    else
+        echo "❌ Failed to install Asta CLI"
+        exit 1
+    fi
+    exit 0
+fi
+
+# Get installed CLI version
+CLI_VERSION=$(asta --version 2>/dev/null | grep -oE '[0-9]+\.[0-9]+\.[0-9]+')
+
+# Compare versions
+if [ "$CLI_VERSION" != "$PLUGIN_VERSION" ]; then
+    echo "🔄 Updating Asta CLI from $CLI_VERSION to $PLUGIN_VERSION..."
+    if uv tool install --force "$INSTALL_URL"; then
+        echo "✅ Asta CLI updated to $PLUGIN_VERSION successfully"
+    else
+        echo "❌ Failed to update Asta CLI"
+        exit 1
+    fi
+fi

plugins/asta-preview/hooks/hooks.json

@@ -7,6 +7,10 @@
           {
             "type": "command",
             "command": "mkdir -p ~/.asta/literature"
+          },
+          {
+            "type": "command",
+            "command": "bash ${CLAUDE_PLUGIN_ROOT}/hooks/sync-cli-version.sh"
           }
         ]
       }

plugins/asta-preview/hooks/sync-cli-version.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+# Check if asta CLI version matches the plugin version and auto-install/update if needed
+
+PLUGIN_VERSION=0.8.1
+INSTALL_URL="git+https://github.com/allenai/asta-plugins.git@v$PLUGIN_VERSION"
+
+# Check if asta is installed
+if ! command -v asta &> /dev/null; then
+    echo "📦 Installing Asta CLI version $PLUGIN_VERSION..."
+    if uv tool install "$INSTALL_URL"; then
+        echo "✅ Asta CLI $PLUGIN_VERSION installed successfully"
+    else
+        echo "❌ Failed to install Asta CLI"
+        exit 1
+    fi
+    exit 0
+fi
+
+# Get installed CLI version
+CLI_VERSION=$(asta --version 2>/dev/null | grep -oE '[0-9]+\.[0-9]+\.[0-9]+')
+
+# Compare versions
+if [ "$CLI_VERSION" != "$PLUGIN_VERSION" ]; then
+    echo "🔄 Updating Asta CLI from $CLI_VERSION to $PLUGIN_VERSION..."
+    if uv tool install --force "$INSTALL_URL"; then
+        echo "✅ Asta CLI updated to $PLUGIN_VERSION successfully"
+    else
+        echo "❌ Failed to update Asta CLI"
+        exit 1
+    fi
+fi

plugins/asta-preview/skills/experiment/SKILL.md

@@ -9,7 +9,6 @@ allowed-tools:
   - Read(.asta/experiment/*)
   - TaskOutput
 ---
-
 # Run Experiments
 
 Run a computational experiment. Given a research question that can be answered via software,
@@ -19,11 +18,18 @@ This skill can also be used to analyze experimental data and generate a research
 
 ## Installation
 
-If `asta` command is not available install it using `uv tool install git+https://github.com/allenai/asta-plugins.git`
+This skill requires the `asta` CLI:
+
+```bash
+# Install/reinstall at the correct version
+PLUGIN_VERSION=0.8.1
+if [ "$(asta --version 2>/dev/null | grep -oE '[0-9]+\.[0-9]+\.[0-9]+')" != "$PLUGIN_VERSION" ]; then
+  uv tool install --force git+https://github.com/allenai/asta-plugins.git@v$PLUGIN_VERSION
+fi
+```
 
 **Prerequisites:** Python 3.11+ and [uv package manager](https://docs.astral.sh/uv/)
 
-Verify installation with `asta experiment --help`
 
 ## Workflow
 

plugins/asta-preview/skills/find-literature/SKILL.md

@@ -12,18 +12,25 @@ allowed-tools:
 
 # Find Literature
 
-Search academic literature for papers relevant to a query. The search will return a ranked list of papers with relevance scores, summaries, and supporting snippets. 
+Search academic literature for papers relevant to a query. The search will return a ranked list of papers with relevance scores, summaries, and supporting snippets.
 
 This is an advanced search, so the query can be long and complex. You may ask the user
 questions to clarify the topic and refine the query before running the search.
 
 ## Installation
 
-If `asta` command is not available install it using `uv tool install git+https://github.com/allenai/asta-plugins.git`
+This skill requires the `asta` CLI:
+
+```bash
+# Install/reinstall at the correct version
+PLUGIN_VERSION=0.8.1
+if [ "$(asta --version 2>/dev/null | grep -oE '[0-9]+\.[0-9]+\.[0-9]+')" != "$PLUGIN_VERSION" ]; then
+  uv tool install --force git+https://github.com/allenai/asta-plugins.git@v$PLUGIN_VERSION
+fi
+```
 
 **Prerequisites:** Python 3.11+ and [uv package manager](https://docs.astral.sh/uv/)
 
-Verify installation with `asta literature --help`
 
 ## Tools Available
 

plugins/asta-preview/skills/pdf-extraction/SKILL.md

@@ -3,10 +3,9 @@ name: PDF Text Extraction
 description: Extract text from PDFs using olmOCR. Use when user asks to "extract text from PDF", "OCR a document", "read a PDF", or needs to process scanned documents.
 allowed-tools:
   - Bash(asta pdf-extraction *)
-  - Bash(olmocr *)
   - Read(.asta/documents/*)
-  - Read(*/markdown/*)
   - Write(.asta/documents/*)
+  - Read(*/markdown/*)
   - Bash(mv *)
   - Bash(cp *)
 ---
@@ -15,11 +14,24 @@ allowed-tools:
 
 Extract high-quality text from PDFs using the [olmOCR](https://github.com/allenai/olmOCR) tool. This skill uses the olmocr CLI for cloud-based OCR processing.
 
-## Quick Start
+## Installation
+
+This skill requires the `asta` CLI:
+
+```bash
+# Install/reinstall at the correct version
+PLUGIN_VERSION=0.8.1
+if [ "$(asta --version 2>/dev/null | grep -oE '[0-9]+\.[0-9]+\.[0-9]+')" != "$PLUGIN_VERSION" ]; then
+  uv tool install --force git+https://github.com/allenai/asta-plugins.git@v$PLUGIN_VERSION
+fi
+```
+
+**Prerequisites:** Python 3.11+ and [uv package manager](https://docs.astral.sh/uv/)
 
-### Extract Text from PDF
 
-The olmocr CLI will auto-install on first use. Basic usage:
+## Quick Start
+
+Basic usage:
 
 ```bash
 # Extract text from a PDF using a temporary workspace
@@ -29,19 +41,23 @@ asta pdf-extraction "$TEMP_WORKSPACE" \
   --markdown
 
 # Output will be in $TEMP_WORKSPACE/markdown/document.md
-```
-
-### Understanding olmocr CLI
-
-The `asta pdf-extraction` command is a passthrough to `olmocr` with this syntax:
 
-```bash
-olmocr <workspace> [OPTIONS]
+# Batch extract text from multiple PDFs
+TEMP_WORKSPACE=$(mktemp -d)
+asta pdf-extraction "$TEMP_WORKSPACE" \
+  --pdfs list-of-pdf-file-paths.txt \
+  --markdown
+
+# Batch extract text from PDFs stored in S3
+TEMP_WORKSPACE=$(mktemp -d)
+asta pdf-extraction "$TEMP_WORKSPACE" \
+  --pdfs s3://my-bucket/prefix/*.pdf \
+  --markdown
 ```
 
 **Key arguments:**
-- `<workspace>` - Output directory (required, positional argument)
-- `--pdfs` - PDF file(s) to process
+- `<workspace>` - Output directory (required: positional argument)
+- `--pdfs` - PDF file(s) to process (required: single path, path with wildcard, S3 path with wildcard, or a text file with paths)
 - `--markdown` - Generate markdown output (recommended)
 - `--workers` - Parallel workers (default: 20)
 

plugins/asta-preview/skills/semantic-scholar/SKILL.md

@@ -7,7 +7,7 @@ allowed-tools:
 
 # Semantic Scholar Lookup
 
-Fast, targeted lookups of paper metadata, citations, and authors using the Semantic Scholar API via `asta papers` commands.
+    Fast, targeted lookups of paper metadata, citations, and authors using the Semantic Scholar API via `asta papers` commands.
 
 ## When to Use This Skill
 
@@ -21,11 +21,17 @@ Fast, targeted lookups of paper metadata, citations, and authors using the Seman
 
 ## Installation
 
-If `asta` command is not available install it using `uv tool install git+https://github.com/allenai/asta-plugins.git`
+This skill requires the `asta` CLI:
 
-**Prerequisites:** Python 3.11+ and [uv package manager](https://docs.astral.sh/uv/)
+```bash
+# Install/reinstall at the correct version
+PLUGIN_VERSION=0.8.1
+if [ "$(asta --version 2>/dev/null | grep -oE '[0-9]+\.[0-9]+\.[0-9]+')" != "$PLUGIN_VERSION" ]; then
+  uv tool install --force git+https://github.com/allenai/asta-plugins.git@v$PLUGIN_VERSION
+fi
+```
 
-Verify installation with `asta papers --help`
+**Prerequisites:** Python 3.11+ and [uv package manager](https://docs.astral.sh/uv/)
 
 ## Available Commands
 

plugins/asta/hooks/hooks.json

@@ -7,6 +7,10 @@
           {
             "type": "command",
             "command": "mkdir -p ~/.asta/literature"
+          },
+          {
+            "type": "command",
+            "command": "bash ${CLAUDE_PLUGIN_ROOT}/hooks/sync-cli-version.sh"
           }
         ]
       }

plugins/asta/hooks/sync-cli-version.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+# Check if asta CLI version matches the plugin version and auto-install/update if needed
+
+PLUGIN_VERSION=0.8.1
+INSTALL_URL="git+https://github.com/allenai/asta-plugins.git@v$PLUGIN_VERSION"
+
+# Check if asta is installed
+if ! command -v asta &> /dev/null; then
+    echo "📦 Installing Asta CLI version $PLUGIN_VERSION..."
+    if uv tool install "$INSTALL_URL"; then
+        echo "✅ Asta CLI $PLUGIN_VERSION installed successfully"
+    else
+        echo "❌ Failed to install Asta CLI"
+        exit 1
+    fi
+    exit 0
+fi
+
+# Get installed CLI version
+CLI_VERSION=$(asta --version 2>/dev/null | grep -oE '[0-9]+\.[0-9]+\.[0-9]+')
+
+# Compare versions
+if [ "$CLI_VERSION" != "$PLUGIN_VERSION" ]; then
+    echo "🔄 Updating Asta CLI from $CLI_VERSION to $PLUGIN_VERSION..."
+    if uv tool install --force "$INSTALL_URL"; then
+        echo "✅ Asta CLI updated to $PLUGIN_VERSION successfully"
+    else
+        echo "❌ Failed to update Asta CLI"
+        exit 1
+    fi
+fi