atomsh 0.1.0__tar.gz

atomsh-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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atomsh-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: atomsh
+Version: 0.1.0
+Summary: Your autonomous coding agent for science
+Author-email: Kamal Choudhary <kchoudh2@jhu.edu>
+License: Apache-2.0
+Project-URL: Homepage, https://atomgpt.org
+Project-URL: Repository, https://github.com/atomgptlab/atomsh
+Keywords: agent,cli,coding-assistant,atomgpt,materials-science,jarvis
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: httpx>=0.24
+Dynamic: license-file
+
+# Atomsh
+
+**Your autonomous coding agent for science.**
+
+Atomsh reads and edits files, searches the codebase, and runs commands from
+your terminal — and it can look a material up while doing it. It runs on
+[AtomGPT](https://atomgpt.org) alone: one account, no other provider.
+
+## Install
+
+```sh
+curl -fsSL https://atomgpt.org/install | bash
+```
+
+The installer uses `uv` when it is present, falls back to a virtualenv, and
+bootstraps `uv` if the system Python is unusable. Everything lands in an
+isolated environment with a launcher in `~/.local/bin`. No sudo.
+
+## Connect
+
+```sh
+atomsh login
+```
+
+This opens atomgpt.org in your browser, you approve once, and the credential
+is stored `0600` in `~/.config/atomsh/auth.json`. On a headless machine use
+`atomsh login --key` and paste an API key instead.
+
+## Use
+
+```sh
+atomsh                            # interactive session
+atomsh "fix the failing test"     # run one prompt and exit
+atomsh -c                         # resume this directory's last session
+git diff | atomsh "review this"   # read a prompt from stdin
+```
+
+| Flag | Effect |
+|------|--------|
+| `-m, --model` | Pick a model (default `gemma-4-26b`) |
+| `-c, --continue` | Resume the most recent session for this directory |
+| `--yolo` | Do not ask before writing files or running commands |
+| `--readonly` | Refuse all writes and shell commands |
+| `--no-materials` | Leave out the AtomGPT materials tools |
+
+Commands: `login`, `logout`, `whoami`, `models`.
+
+In a session: `!<command>` runs a shell command yourself, `/history` replays
+the conversation, `/model` switches model, `/clear` starts a fresh thread.
+**Escape** interrupts a response while it is streaming.
+
+## Permissions
+
+By default atomsh asks before anything that writes a file or runs a
+command; reads and searches happen unattended. Answering `a` allows that tool
+for the rest of the session. A path outside the working directory always
+prompts, even after `a`.
+
+## Models
+
+`atomsh models` lists what your account can use. The `mcp.*` models are
+excluded on purpose: those run the AtomGPT materials agent on the server and
+answer in prose rather than making tool calls, so they cannot drive a coding
+loop. Use them through a chat client instead.
+
+## Tools
+
+`read_file`, `write_file`, `edit_file`, `list_dir`, `glob_files`,
+`grep_files`, `bash`.
+
+### Materials tools
+
+atomsh connects to the AtomGPT MCP server with the same credential and
+carries six more tools by default: `explore`, `build`, `predict`,
+`characterize`, `apply`, `validate`. Each dispatches to a family of AtomGPT apps — JARVIS-DFT lookups,
+ALIGNN predictions, band structures, XRD, interfaces, protein folding — so the
+agent can look a material up instead of answering from the model's memory:
+
+```
+$ atomsh --materials "bandgap of silicon JVASP-1002 from JARVIS-DFT"
+  · explore(app=/jarvis_dft/query, params={"jid": "JVASP-1002"})
+OptB88vdW 0.731 eV · mBJ 1.277 eV · HSE 1.22 eV
+```
+
+The tool list is cached under `~/.local/share/atomsh/` and refreshed daily,
+and the MCP session is opened on first use, so carrying them costs nothing at
+startup. `--no-materials` leaves them out — worth doing for pure coding work,
+where a narrower tool surface is easier for the model.
+
+## Development
+
+```sh
+uv venv && uv pip install -e .
+ATOMSH_API_KEY=sk-… atomsh --readonly "what does this repo do?"
+```
+
+`ATOMSH_API_BASE` points the client at a different deployment.
+
+`install.sh` here is the canonical installer; `atomgpt.org/install` serves a
+copy of it.
+
+## License
+
+Apache-2.0

atomsh-0.1.0/README.md

@@ -0,0 +1,104 @@
+# Atomsh
+
+**Your autonomous coding agent for science.**
+
+Atomsh reads and edits files, searches the codebase, and runs commands from
+your terminal — and it can look a material up while doing it. It runs on
+[AtomGPT](https://atomgpt.org) alone: one account, no other provider.
+
+## Install
+
+```sh
+curl -fsSL https://atomgpt.org/install | bash
+```
+
+The installer uses `uv` when it is present, falls back to a virtualenv, and
+bootstraps `uv` if the system Python is unusable. Everything lands in an
+isolated environment with a launcher in `~/.local/bin`. No sudo.
+
+## Connect
+
+```sh
+atomsh login
+```
+
+This opens atomgpt.org in your browser, you approve once, and the credential
+is stored `0600` in `~/.config/atomsh/auth.json`. On a headless machine use
+`atomsh login --key` and paste an API key instead.
+
+## Use
+
+```sh
+atomsh                            # interactive session
+atomsh "fix the failing test"     # run one prompt and exit
+atomsh -c                         # resume this directory's last session
+git diff | atomsh "review this"   # read a prompt from stdin
+```
+
+| Flag | Effect |
+|------|--------|
+| `-m, --model` | Pick a model (default `gemma-4-26b`) |
+| `-c, --continue` | Resume the most recent session for this directory |
+| `--yolo` | Do not ask before writing files or running commands |
+| `--readonly` | Refuse all writes and shell commands |
+| `--no-materials` | Leave out the AtomGPT materials tools |
+
+Commands: `login`, `logout`, `whoami`, `models`.
+
+In a session: `!<command>` runs a shell command yourself, `/history` replays
+the conversation, `/model` switches model, `/clear` starts a fresh thread.
+**Escape** interrupts a response while it is streaming.
+
+## Permissions
+
+By default atomsh asks before anything that writes a file or runs a
+command; reads and searches happen unattended. Answering `a` allows that tool
+for the rest of the session. A path outside the working directory always
+prompts, even after `a`.
+
+## Models
+
+`atomsh models` lists what your account can use. The `mcp.*` models are
+excluded on purpose: those run the AtomGPT materials agent on the server and
+answer in prose rather than making tool calls, so they cannot drive a coding
+loop. Use them through a chat client instead.
+
+## Tools
+
+`read_file`, `write_file`, `edit_file`, `list_dir`, `glob_files`,
+`grep_files`, `bash`.
+
+### Materials tools
+
+atomsh connects to the AtomGPT MCP server with the same credential and
+carries six more tools by default: `explore`, `build`, `predict`,
+`characterize`, `apply`, `validate`. Each dispatches to a family of AtomGPT apps — JARVIS-DFT lookups,
+ALIGNN predictions, band structures, XRD, interfaces, protein folding — so the
+agent can look a material up instead of answering from the model's memory:
+
+```
+$ atomsh --materials "bandgap of silicon JVASP-1002 from JARVIS-DFT"
+  · explore(app=/jarvis_dft/query, params={"jid": "JVASP-1002"})
+OptB88vdW 0.731 eV · mBJ 1.277 eV · HSE 1.22 eV
+```
+
+The tool list is cached under `~/.local/share/atomsh/` and refreshed daily,
+and the MCP session is opened on first use, so carrying them costs nothing at
+startup. `--no-materials` leaves them out — worth doing for pure coding work,
+where a narrower tool surface is easier for the model.
+
+## Development
+
+```sh
+uv venv && uv pip install -e .
+ATOMSH_API_KEY=sk-… atomsh --readonly "what does this repo do?"
+```
+
+`ATOMSH_API_BASE` points the client at a different deployment.
+
+`install.sh` here is the canonical installer; `atomgpt.org/install` serves a
+copy of it.
+
+## License
+
+Apache-2.0

atomsh-0.1.0/atomsh/__init__.py

@@ -0,0 +1,6 @@
+"""Atomsh — your autonomous coding agent for science.
+
+Installed as the `atomsh` command; entry point is `atomsh.cli:main`.
+"""
+
+__version__ = "0.1.0"

atomsh-0.1.0/atomsh/agent.py

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+"""The agent loop: model → tool calls → tool results → model, until it stops."""
+
+import json
+from pathlib import Path
+
+from . import tools as toolkit
+from .client import AtomGPT, AtomGPTError
+from .config import MAX_STEPS
+from .interrupt import escape_watch
+from .permissions import ALLOW, Permissions
+from .prompt import system_prompt
+
+DIM = "\033[2m"
+BOLD = "\033[1m"
+RESET = "\033[0m"
+
+
+class Agent:
+    """Drives one conversation against one model with one tool set."""
+
+    def __init__(self, client: AtomGPT, model: str, session,
+                 permissions: Permissions = None, root: Path = None,
+                 color: bool = True, remote=None):
+        self.client = client
+        self.model = model
+        self.session = session
+        self.root = root or Path.cwd()
+        self.permissions = permissions or Permissions("ask", self.root)
+        self.color = color
+        # An MCPClient, when --materials is on. Its tools sit alongside the
+        # local ones; the model does not need to know which is which.
+        self.remote = remote
+        self.remote_tools = set()
+        self.tool_schema = list(toolkit.SCHEMA)
+        if remote is not None:
+            remote_schema = remote.schema()
+            self.remote_tools = {t["function"]["name"] for t in remote_schema}
+            self.tool_schema += remote_schema
+        if not self.session.messages:
+            self.session.messages.append({
+                "role": "system",
+                "content": system_prompt(str(self.root),
+                                         materials=remote is not None),
+            })
+
+    def _dim(self, text: str) -> str:
+        return f"{DIM}{text}{RESET}" if self.color else text
+
+    def run(self, user_text: str) -> str:
+        """Run one user turn to completion. Returns the final assistant text."""
+        self.session.messages.append({"role": "user", "content": user_text})
+        final = ""
+
+        for _ in range(MAX_STEPS):
+            # `last` doubles as "have we printed anything this step": stripped
+            # channel markers leave stray blank lines, so leading whitespace is
+            # swallowed and the closing newline is only added if one is missing.
+            state = {"last": ""}
+
+            def on_text(piece, state=state):
+                if not state["last"] and not piece.strip():
+                    return
+                state["last"] = piece
+                print(piece, end="", flush=True)
+
+            try:
+                with escape_watch() as cancelled:
+                    result = self.client.stream(
+                        self.session.messages, self.tool_schema, self.model,
+                        on_text=on_text, cancelled=cancelled,
+                    )
+            except AtomGPTError as e:
+                print(f"\n{self._dim('error:')} {e}")
+                return ""
+
+            message = result["message"]
+            if state["last"] and not state["last"].endswith("\n"):
+                print()
+            self.session.messages.append(message)
+            self.session.save()
+
+            if result.get("finish_reason") == "cancelled":
+                print(self._dim("  interrupted"))
+                return message.get("content") or ""
+
+            calls = message.get("tool_calls")
+            if not calls:
+                final = message.get("content") or ""
+                if not final and not state["last"]:
+                    print(self._dim("(no response — try rephrasing)"))
+                return final
+
+            for call in calls:
+                self._run_tool(call)
+            self.session.save()
+
+        print(self._dim(f"stopped after {MAX_STEPS} steps"))
+        return final
+
+    def _run_tool(self, call: dict) -> None:
+        """Execute one tool call and append its result to the conversation."""
+        name = (call.get("function") or {}).get("name") or ""
+        raw_args = (call.get("function") or {}).get("arguments") or "{}"
+        try:
+            args = json.loads(raw_args) if raw_args.strip() else {}
+        except ValueError:
+            args = {}
+
+        handler = toolkit.HANDLERS.get(name)
+        if handler is None and name not in self.remote_tools:
+            return self._reply(call, f"Error: no such tool {name!r}.")
+
+        decision, reason = self.permissions.check(name, args)
+        if decision != ALLOW:
+            print(self._dim(f"  ✗ {name} — {reason}"))
+            return self._reply(call, f"Denied: {reason}")
+
+        print(self._dim(f"  · {name}({self._summarize(args)})"))
+        try:
+            if handler is None:
+                output = self.remote.call(name, args)
+            else:
+                output = handler(self.root, **args)
+        except TypeError as e:
+            output = f"Error: bad arguments for {name}: {e}"
+        except Exception as e:  # a tool must never kill the session
+            output = f"Error: {name} raised {type(e).__name__}: {e}"
+        self._reply(call, output)
+
+    def _reply(self, call: dict, content: str) -> None:
+        self.session.messages.append({
+            "role": "tool",
+            "tool_call_id": call.get("id") or "",
+            "content": content,
+        })
+
+    @staticmethod
+    def _summarize(args: dict) -> str:
+        """One-line rendering of tool arguments for the activity log."""
+        parts = []
+        for key, value in args.items():
+            text = value if isinstance(value, str) else json.dumps(value)
+            text = text.replace("\n", " ")
+            if len(text) > 60:
+                text = text[:60] + "…"
+            parts.append(f"{key}={text}")
+        return ", ".join(parts)