@mantra-ai/cli 0.1.8 → 0.1.10

package/README.md

@@ -2,7 +2,7 @@
 
 The open-source hypothesis generator hooked to Claude Code.
 
-Add papers by DOI, PMID, arXiv ID, or PDF file. Mantra resolves metadata, fetches open-access full text, and normalizes everything into a structured local library backed by SQLite.
+Discover papers across your Zotero library, local PDFs, and the mantra store. Mantra resolves metadata, fetches open-access full text, and normalizes everything into a structured local library backed by SQLite.
 
 ## Install
 
@@ -15,38 +15,52 @@ Supports macOS (Apple Silicon & Intel) and Linux (x64 & ARM64).
 ## Quick start
 
 ```bash
-mantra add 10.1038/s41586-024-07487-w   # add by DOI
-mantra add paper.pdf                     # add from a local PDF
-mantra init "my-review"                  # start a project in the current directory
-mantra discover 10.1038/s41586-024-07487-w  # find by ID and add to project
-mantra discover CRISPR off-target        # search library, pick papers to add
-mantra papers                            # list papers
-mantra search "CRISPR"                   # full-text search
+mantra init "my-review"                  # start a project
+mantra discover CRISPR off-target        # search all sources, pick papers to add
+mantra discover 10.1038/s41586-024-07487-w  # add by DOI directly
+mantra hypothesize                       # generate hypotheses from project papers
 ```
 
-### Batch ingestion
+### Discover
 
-Pass multiple identifiers in a single command to ingest papers in bulk:
+`discover` is the primary way to find and add papers to a project. It searches across all configured sources transparently:
+
+- **Mantra store** — papers you've previously added
+- **Zotero catalog** — title and author search in your Zotero library
+- **PDF directories** — indexed PDFs with extracted DOIs
 
 ```bash
-mantra add 10.1038/s41586-024-07487-w 10.1126/science.adg7879 PMC9876543 arXiv:2301.07041
+mantra discover genome editing techniques    # search all sources
+mantra discover --select all CRISPR          # add all matches non-interactively
+mantra discover --select 1,3 protein folding # add specific results
+mantra discover 10.1234/example 2301.07041   # add by DOI or arXiv ID
 ```
 
-You can also read identifiers from a file (one per line):
+Results from multiple sources are merged by DOI, so a paper in both your Zotero and mantra store appears once. When you select a paper from Zotero or a PDF directory, it's automatically ingested into the mantra store and linked to your project.
+
+### Direct ingestion
+
+Use `add` to ingest papers directly without a project context:
 
 ```bash
-mantra add --file dois.txt --delay 500
+mantra add 10.1038/s41586-024-07487-w   # add by DOI
+mantra add paper.pdf                     # add from a local PDF
 ```
 
-The `--delay` flag sets a pause between requests (in ms) to avoid rate limits.
+### Batch ingestion
+
+```bash
+mantra add 10.1038/s41586-024-07487-w 10.1126/science.adg7879 PMC9876543 arXiv:2301.07041
+mantra add --file dois.txt --delay 500   # from file, with rate limiting
+```
 
 ## Commands
 
 | Command | Description |
 |---|---|
-| `add [inputs...]` | Add papers by DOI, PMID, PMCID, arXiv ID, or PDF path |
 | `init <name>` | Initialize a project in the current directory |
-| `discover [inputs...]` | Find papers by ID or search and add to current project |
+| `discover [inputs...]` | Find papers across all sources and add to current project |
+| `add [inputs...]` | Add papers by DOI, PMID, PMCID, arXiv ID, or PDF path |
 | `papers` | List papers in the library or current project |
 | `show <id>` | Show full details for a paper |
 | `search <query>` | Full-text search with snippets |
@@ -70,19 +84,18 @@ When you add a paper, Mantra:
 
 ### Supported sources
 
-Crossref, OpenAlex, EuropePMC, bioRxiv, medRxiv, arXiv, PLOS.
+Crossref, OpenAlex, EuropePMC, bioRxiv, medRxiv, arXiv, PLOS, Zotero (local).
 
 ## Projects
 
-Mantra organizes papers into per-directory projects, similar to how git works with repositories. Run `mantra init` in any directory to create a project, then use `discover` to find and link papers.
+Mantra organizes papers into per-directory projects. Run `mantra init` to create a project, then use `discover` to find and curate papers from all your sources.
 
 ```bash
 mkdir my-review && cd my-review
 mantra init "my-review"
-mantra discover 10.1234/example              # add by ID
-mantra discover genome editing techniques    # search library + pick interactively
-mantra discover --select all genome editing  # add all matches non-interactively
-mantra papers --project                      # list only this project's papers
+mantra discover protein aggregation     # searches Zotero, PDFs, and mantra store
+mantra discover --select all amyloid    # add all matches non-interactively
+mantra papers --project                 # list this project's papers
 ```
 
 ## Configuration
@@ -93,6 +106,17 @@ mantra config set key val   # set a config value
 mantra config path          # show config file location
 ```
 
+### Source configuration
+
+Configure local sources so `discover` can search across them:
+
+```bash
+mantra config set zoteroPath ~/Zotero     # Zotero data directory
+mantra config set pdfDirs ~/Papers        # PDF directories to index
+```
+
+These are auto-detected during `mantra setup` if Zotero is installed.
+
 ### API keys
 
 For PDF-to-structured-text conversion (when JATS XML is unavailable), set a Gemini API key:

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mantra-ai/cli",
-  "version": "0.1.8",
+  "version": "0.1.10",
   "description": "The open-source hypothesis generator hooked to Claude Code",
   "license": "MIT",
   "bin": {
@@ -10,9 +10,9 @@
     "bin/mantra"
   ],
   "optionalDependencies": {
-    "@mantra-ai/cli-darwin-arm64": "0.1.8",
-    "@mantra-ai/cli-darwin-x64": "0.1.8",
-    "@mantra-ai/cli-linux-x64": "0.1.8",
-    "@mantra-ai/cli-linux-arm64": "0.1.8"
+    "@mantra-ai/cli-darwin-arm64": "0.1.10",
+    "@mantra-ai/cli-darwin-x64": "0.1.10",
+    "@mantra-ai/cli-linux-x64": "0.1.10",
+    "@mantra-ai/cli-linux-arm64": "0.1.10"
   }
 }