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1-7 of 7claude-science/changelog Changed · +15 / -0 lines
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33> Release notes for Claude Science, including new features, improvements, and bug fixes by version.
44
5<Update label="0.1.56" description="October 2, 2026">
6 * Excel (.xlsx) previews now show cell colors, bold text, and color-scale heat maps
7 * Reviewer findings now open in place, with a button to the reviewer's full transcript
8 * A stalled file upload now stops by itself, and a failed upload says why under the file
9 * Skills: "Check for updates…" now lists only the imported skills whose files changed
10 * Claude now asks before it uses a tool from a connector that your organization's plugins add
11 * Fixed a case where the app could delete a skill from your computer when it started
12 * Windows: zoom the app window with Ctrl+Plus and Ctrl+Minus, and reset it with Ctrl+0
13 * Windows: IT teams can now deploy package mirror credentials as a `.netrc` file, as on Mac and Linux
14 * Mac: the app now applies only a fixed list of variables from the `env` file in the data folder; move a GitHub token to **Settings > Credentials**
15 * Admins can now turn off Claude's web search tool with `enable_web_search = false` in `config.toml`
16 * Security hardening of the analysis sandbox on Mac, Windows, and Linux
17 * Various bug fixes and security improvements
18</Update>
19
520<Update label="0.1.55" description="September 29, 2026">
621 * New sessions on an organization's default model with more life sciences restrictions now show a notice with a one-click switch to another model
722 * Fixed an error Claude ran into when outlining an existing multi-panel figure or drafting a paper's brief from its abstract and figure captions
claude-science/command-line-settings Changed · +6 / -1 lines
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8585
8686`DO_NOT_TRACK`, set to any value other than `0` or `false`, turns usage analytics and error reports off. It is the same switch as `disable_telemetry = true` in the configuration file. `GITHUB_TOKEN` (or `GH_TOKEN`) is optional and is used only against `api.github.com`, to lift the rate limit when you install a skill from a GitHub repository. Claude Science also reads the standard proxy variables (`HTTPS_PROXY`, `HTTP_PROXY`, `NO_PROXY`, and `ALL_PROXY`); see [Use Claude Science on a corporate network](/docs/claude-science/corporate-networks#connect-through-an-outbound-proxy). The proxy address variables are the one case where the environment overrides the configuration file, and `NO_PROXY` is merged with the `no_proxy` key rather than replacing it. Every other setting belongs in the configuration file.
8787
88An app started from the macOS Dock or Finder, or from the Windows Start menu, does not see variables exported in a terminal. The macOS app reads the `env` file in the data directory (by default `~/.claude-science/env`) when it starts, so put the variable there as a `KEY=VALUE` line, then quit and reopen the app. On Windows, set it as a user environment variable, then quit and reopen the app. See [How the environment variables reach the app](/docs/claude-science/corporate-networks#how-the-environment-variables-reach-the-app).
88An app started from the macOS Dock or Finder, or from the Windows Start menu, does not see variables exported in a terminal.
89
90* **macOS**: the app reads the `env` file in the data directory (by default `~/.claude-science/env`) when it starts. It applies only a fixed list of variables from the file, which includes `DO_NOT_TRACK` and the proxy variables but not `GITHUB_TOKEN` or `GH_TOKEN`. Put `DO_NOT_TRACK` or a proxy variable there as a `KEY=VALUE` line, then quit and reopen the app. Add a GitHub token under **Settings > Credentials** instead, and delete its line from the file. Before version 0.1.56, the file could set any variable.
91* **Windows**: set the variable as a user environment variable, then quit and reopen the app.
92
93See [How the environment variables reach the app](/docs/claude-science/corporate-networks#how-the-environment-variables-reach-the-app).
8994
9095## See also
9196
claude-science/configuration-file-reference Changed · +16 / -1 lines
## Web search and upload keys
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11# Configuration file reference
22
3> Claude Science's config.toml file: where it lives, how its values interact with the Settings page, and the network-related keys for the outbound proxy, certificate bundles, package mirror, and sandbox network allowlist.
3> Claude Science's config.toml file: where it lives, how it interacts with Settings, and its network, web search, and upload keys.
44
55Claude Science reads optional settings from a TOML file named `config.toml` in its default data folder, which is `~/.claude-science/config.toml` on macOS and Linux and `%USERPROFILE%\.claude-science\config.toml` on Windows. Every key has a default, so the app starts with no file present; administrators deploy the file with device management to set fleet policy. The file is read once at startup, so changes take effect after a restart. The `claude-science` command accepts `--config <file>` to read a different file for one run.
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4242| `enabled` | boolean | `true` | When `false`, code Claude runs has no network access: package installs and data fetches inside the analysis fail, while the app's own connections are unaffected. This is a no-network mode, not a way to skip the allowlist. |
4343| `allowed_domains` | array of strings | `[]` | Domains added to the built-in allowlist, as exact hostnames or wildcards such as `*.example.org`. While the organization manages the [network allowlist](/docs/claude-science/admin-controls#network-allowlist) under **Organization settings** > **Claude Science**, these domains are set aside and the organization's list applies. |
4444| `denied_domains` | array of strings | `[]` | Domains added to the built-in denylist. A denied domain is blocked even if it also appears on the allowlist, and the built-in denylist entries cannot be removed. |
45
46## Web search and upload keys
47
48Put `enable_web_search`, `chunked_upload_threshold_bytes`, or both at the top of `config.toml`, above the first line in square brackets such as `[network]`, as in this example:
49
50```toml theme={null}
51# Turn off Claude's web search tool.
52enable_web_search = false
53
54# Upload attached files larger than 4 MiB in 5 MiB chunks (an example value for a proxy that limits requests to 8 MiB).
55chunked_upload_threshold_bytes = 4194304
56```
57
58* **`enable_web_search`** (default `true`): `false` turns off Claude's web search tool. Literature search, connectors, and the sites that code in the sandbox can reach are unaffected.
59* **`chunked_upload_threshold_bytes`** (default `47185920`, 45 MiB): Claude Science uploads an attached file larger than this value in 5 MiB chunks instead of one request. When a reverse proxy in front of Claude Science limits request size, set it below that limit, and keep that limit above 5 MiB. A value above the default prevents Claude Science from starting.
4560
4661## Related resources
4762
claude-science/corporate-networks Changed · +56 / -8 lines
### Deploy the mirror credential as a file ### Mirror sign-in fails with a deployed credential file
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3434| TLS inspection on pip package downloads | Supported, with the corporate root also installed in the operating system's trust store (see [Corporate root for package downloads](#corporate-root-for-package-downloads)) | Supported automatically through the Windows certificate store | Supported, with the corporate root also installed in the operating system's trust store (see [Corporate root for package downloads](#corporate-root-for-package-downloads)) |
3535| Internal package mirror (Artifactory, Nexus) | Supported | Supported | Supported |
3636| Internal package mirror reached only through the corporate proxy | Not supported | Not supported | Not supported |
37| Authenticated package mirror | Supported, with the credential saved in Settings | Supported, with the credential saved in Settings | Supported, with the credential saved in Settings |
37| Authenticated package mirror | Supported, with the credential saved in Settings or in a file you deploy | Supported, with the credential saved in Settings or, with version 0.1.56 or later, in a file you deploy | Supported, with the credential saved in Settings or in a file you deploy |
3838| Local connectors (the bundled research tools) behind TLS inspection | Not supported | Not supported | Not supported |
3939
4040## Point package installs at an internal mirror
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4141
4242When your network blocks the public package hosts (`conda.anaconda.org`, `repo.anaconda.com`, `pypi.org`), point Claude Science at your internal artifact repository instead, and every environment build fetches packages through it. You can set the mirror in three places: once for the whole organization under **Organization settings** > **Claude Science** > **Organization package mirror**, for a fleet with the `[conda] channel_mirror` and `pip_index_url` keys in a [deployed `config.toml`](/docs/claude-science/manage-on-devices#deploy-configuration-with-device-management), or for a single machine under **Settings** > **Network** > **Package mirror**, where the same two settings are called the conda channel mirror and the pip index URL. The steps below use the Settings page, the quickest way to test a mirror URL before you deploy it.
4343
44The organization setting takes a conda channel URL and a Python package index (PyPI) URL, which apply to every member whether or not the organization manages the network allowlist. They take precedence over a mirror set in a member's configuration file or Settings; the member's values are kept but not used, and their Settings show the package mirror as controlled by their admin. The same URL rules apply as below, and an address that breaks those rules is ignored for that registry rather than stopping the app. Members still sign in to the mirror themselves, once for each mirror host (see [Mirror credentials](#mirror-credentials)), and the mirror removes the public hosts it replaces for every member. See [Organization package mirror](/docs/claude-science/admin-controls#organization-package-mirror).
44The organization setting takes a conda channel URL and a Python package index (PyPI) URL, which apply to every member whether or not the organization manages the network allowlist. They take precedence over a mirror set in a member's configuration file or Settings; the member's values are kept but not used, and their Settings show the package mirror as controlled by their admin. The same URL rules apply as below, and an address that breaks those rules is ignored for that registry rather than stopping the app. Members still sign in to the mirror themselves, once for each mirror host (see [Mirror credentials](#mirror-credentials)), unless you [deploy the credential as a file](#deploy-the-mirror-credential-as-a-file). The mirror removes the public hosts it replaces for every member. See [Organization package mirror](/docs/claude-science/admin-controls#organization-package-mirror).
4545
4646Set both a conda channel mirror and a pip index: analysis environments are built from conda packages, so a pip index alone leaves the first build stuck trying to reach the public conda host.
4747
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5555 </Step>
5656
5757 <Step title="Save, then run the check">
58 Select **Save**, then **Check**: a green result confirms the mirror answered, and a `401` or `403` on an authenticated mirror is expected until a credential is saved (see [Mirror credentials](#mirror-credentials)). The mirror takes effect for the next package operation without a restart. On a machine with an outbound proxy, confirm with a test environment build rather than the check alone (see [Mirror traffic and your other network controls](#mirror-traffic-and-your-other-network-controls)).
58 Select **Save**, then **Check**: a green result confirms the mirror answered, and a `401` or `403` on an authenticated mirror is expected until a credential is saved or, on Windows, deployed as a file (see [Mirror credentials](#mirror-credentials)). The mirror takes effect for the next package operation without a restart. On a machine with an outbound proxy, confirm with a test environment build rather than the check alone (see [Mirror traffic and your other network controls](#mirror-traffic-and-your-other-network-controls)).
5959 </Step>
6060</Steps>
6161
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8383
8484### Mirror credentials
8585
86For a mirror that requires authentication, enter one username and access token under **Settings** > **Network** > **Package mirror** > **Mirror credentials**, using an account scoped to reading the mirror, then run the check so it signs in with the credential. The one credential is presented to both the conda-mirror host and the pip-index host, so if those need different accounts, keep one of them anonymous; the credential is sent only to `https://` mirror hosts.
86For a mirror that requires authentication, enter one username and access token under **Settings > Network > Package mirror > Mirror credentials**, using an account scoped to reading the mirror. If you entered the mirror address in Settings, run the check so that it signs in with the credential. The one credential is presented to both the conda-mirror host and the pip-index host, so if those need different accounts, keep one of them anonymous; the credential is sent only to `https://` mirror hosts.
8787
88Claude Science stores the credential encrypted in its local database, using a key kept in a file only the member's account can read (on macOS, a copy of that key is in the keychain for recovery), and also writes the credential, automatically, to a plaintext `.netrc` at `~/.claude-science/conda/.netrc` that the conda and pip download tools read during environment builds. Code that runs while an environment builds (a package's `setup.py`, for example) can read that file, Claude's analysis code cannot read either location, and a `.netrc` in the member's home directory is not used for these downloads. For a macOS or Linux fleet that manages credentials centrally, deploy that `.netrc` file yourself instead (on Windows, save the credential in Settings), one `machine <mirror hostname>` block per mirror host with `login` and `password` lines and no comments, and use either the file or Settings, not both: a credential saved in Settings rewrites the file from the saved value at the save and at every restart and environment build, while a file deployed with no credential saved in Settings is left alone.
88Claude Science stores the credential encrypted in its local database, using a key kept in a file only the member's account can read (on macOS, a copy of that key is in the keychain for recovery), and also writes the credential, automatically, to a plaintext `.netrc` at `~/.claude-science/conda/.netrc` that the conda and pip download tools read during environment builds. Code that runs while an environment builds (a package's `setup.py`, for example) can read that file, Claude's analysis code cannot read either location while the sandbox is on (the default), and a `.netrc` in the member's home directory is not used for these downloads. To manage credentials centrally instead, see [Deploy the mirror credential as a file](#deploy-the-mirror-credential-as-a-file).
8989
9090Environments a member registers from an existing project folder install their packages inside the analysis sandbox during a session, where the credential is hidden by design, so those environments need a mirror that allows anonymous reads.
9191
92### Deploy the mirror credential as a file
93
94To manage mirror credentials centrally, deploy a `.netrc` file to each member's profile:
95
96* **macOS and Linux**: `~/.claude-science/conda/.netrc`
97* **Windows, version 0.1.56 or later**: `%USERPROFILE%\.claude-science\conda\.netrc`
98
99<Note>
100 On Windows, a deployment tool that runs as an administrator or as the system account needs the member's full path, such as `C:\Users\ada\.claude-science\conda\.netrc`.
101</Note>
102
103Write one block like this for each mirror host:
104
105```text theme={null}
106machine yourorg.jfrog.io
107login mirror-reader
108password EXAMPLE-TOKEN
109```
110
111Create the `.claude-science` and `conda` folders if they don't exist, and let the member read the file and write to both folders. On Windows, the sandbox relies on this to keep the file from Claude's code and connectors. On macOS and Linux, make the member the owner of the file and both folders, and set the file's permissions to `600`.
112
113Before you deploy, have members select **Remove** under **Settings > Network > Package mirror > Mirror credentials** when that button shows, and keep **Mirror credentials** empty, even when a **Finish setting up package access** notice shows. Claude Science can write a saved credential over the file. Deploy the file before members install or update Claude Science.
114
115Before rollout, test the file on one machine where Claude Science has never run:
116
1171. Deploy the file for a member with a standard account.
1182. Install Claude Science, sign in as that member, and let environment setup finish.
1193. Look in your mirror's request log for the file's login on both the Python index and the conda channel.
120
121If the test doesn't pass, see [Mirror sign-in fails with a deployed credential file](#mirror-sign-in-fails-with-a-deployed-credential-file).
122
123To rotate the token, deploy the file again, and on Linux have members quit and reopen Claude Science so that the sandbox hides the new file.
124
92125### Mirror traffic and your other network controls
93126
94127Configuring a mirror removes the public package hosts from the sandbox's network allowlist and admits the mirror host in their place, so a misconfigured mirror fails with an error that names the mirror rather than falling back to the public hosts. To keep the public hosts reachable alongside the mirror, re-add them under **Settings > Network** (`pypi.org` and `files.pythonhosted.org` for pip, and `conda.anaconda.org`, `repo.anaconda.com`, and `anaconda.org` for conda). **Network** settings accept exact hostnames only. To allow subdomains as well, add `*.pypi.org` and `*.anaconda.org` to `[sandbox.network] allowed_domains` in `config.toml`. When the organization manages the network allowlist, **Network** settings are read-only, so a member can't re-add them, and the hosts a mirror replaces stay removed even if they are switched on in the organization's list.
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134167
135168How the variables reach the app depends on the operating system:
136169
137* On macOS, the Claude Science app reads a file named `env` in its data folder (`~/.claude-science/env` unless you moved the data folder) when it launches. The file holds `KEY=VALUE` lines (`export KEY=VALUE` also works). Put the three variables there, then quit and reopen the app; an app started from the Dock or Finder does not see variables exported in a terminal. The file's `NO_PROXY` entries merge with the other sources rather than replacing them.
170* On macOS, the Claude Science app reads a file named `env` in its data folder (`~/.claude-science/env` unless you moved the data folder) when it launches. The file holds `KEY=VALUE` lines (`export KEY=VALUE` also works). Put the three proxy variables there, then quit and reopen the app; an app started from the Dock or Finder does not see variables exported in a terminal. The file's `NO_PROXY` entries merge with the other sources rather than replacing them.
171
172 The app applies only a fixed list of variables from this file, which includes the proxy variables and `DO_NOT_TRACK`, and skips any other line with a warning in `~/.claude-science/logs/app.log`. A `GITHUB_TOKEN` line, for example, is skipped, so add the token under **Settings > Credentials** (see [Environment variables](/docs/claude-science/command-line-settings#environment-variables)). Before version 0.1.56, the file could set any variable.
138173* On Windows, the app reads the variables from the user's environment when it starts, so set them as user environment variables, then quit Claude Science from its notification-area icon and open it again; variables typed into an open Command Prompt or PowerShell window do not reach an app started from the Start menu. Because Claude Science already follows Windows proxy settings, most PCs need no variables, and `[network] proxy` in `config.toml` is the form to deploy.
139174* On Linux, export the variables in the shell or service unit that starts `claude-science serve`. The `env` file is read only by the macOS app.
140175
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207242
208243### HTTP 401 on the mirror check
209244
210With no saved credential, a `401` is expected because the check sends none; enter the credential under **Mirror credentials** and run the check again. When a credential is saved, the check signs in with it, so a `401` means the token is wrong or expired. On a proxy-configured machine the check and a build can also take different network paths (see [Mirror traffic and your other network controls](#mirror-traffic-and-your-other-network-controls)).
245When no credential is saved in Settings, the check sends a credential on Windows only, taken from a deployed `.netrc` file's entry for that mirror host. With none saved, the check sends no credential on macOS and Linux, or on Windows when no deployed file has an entry for that mirror host. A `401` or `403` is then expected, even when builds sign in with the file. The **Check** button shows beside a mirror address entered in Settings, not beside one that the organization or a deployed `config.toml` sets.
246
247* **Your fleet deploys the `.netrc` file**: leave **Mirror credentials** empty and confirm the file as described under [Deploy the mirror credential as a file](#deploy-the-mirror-credential-as-a-file).
248* **You save the credential in Settings**: enter it under **Settings > Network > Package mirror > Mirror credentials** and run the check again.
249
250When the check does sign in, a `401` means the token is wrong or expired. On a proxy-configured machine the check and a build can also take different network paths (see [Mirror traffic and your other network controls](#mirror-traffic-and-your-other-network-controls)).
251
252### Mirror sign-in fails with a deployed credential file
253
254When a `.netrc` file you deployed (see [Deploy the mirror credential as a file](#deploy-the-mirror-credential-as-a-file)) doesn't work, find the case that matches:
255
256* **An environment build fails with `401` or `403`**: check the file's name, contents, permissions, and token (see [HTTP 401 or 403 during an environment build](#http-401-or-403-during-an-environment-build)). On Windows, Claude Science doesn't use a file it can't open or whose keywords or characters it doesn't accept, and Python package installs then don't sign in with it. In a terminal, `claude-science logs` says why.
257* **Your mirror's request log shows nothing**: if your network also allows the public package hosts, setup can use them before the organization's mirror address arrives. In that case, set the mirror in `config.toml` (see [Configuration file reference](/docs/claude-science/configuration-file-reference)) on another machine where Claude Science has never run, before the install, and repeat the test.
258* **The file reached a machine while a credential was still saved**: have the member select **Remove** under **Settings > Network > Package mirror > Mirror credentials**, then deploy the file again, because removing can empty it. On Windows, have the member then quit Claude Science from its notification-area icon and open it again.
211259
212260### Green check, then nothing provides the package
213261
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159159
160160An organization mirror takes precedence over a mirror a member set in Settings or in their configuration file. The member's values are kept but not used, and their Settings show that the package mirror is controlled by their admin. The mirror host is allowed automatically and the public hosts it replaces are removed from the allowlist, as for a member-set mirror. While you manage the network allowlist, those hosts stay removed even if they are switched on in your list.
161161
162Mirror credentials stay with each member. A member signs in to your mirror once per mirror host under **Settings** > **Network** > **Package mirror** > **Mirror credentials**, and the organization settings never store a credential.
162Mirror credentials stay with each member. A member signs in to your mirror once per mirror host under **Settings > Network > Package mirror > Mirror credentials**, unless you [deploy the credential as a file](/docs/claude-science/corporate-networks#deploy-the-mirror-credential-as-a-file), and the organization settings never store a credential.
163163
164164### SSH hosts
165165
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243243| - | - | - |
244244| Connectors > connectors you add for your organization | Supported in Claude Science | Connectors you add on the **Connectors** page, from the directory or by web address (custom connectors), are available to members in the app, as in claude.ai. Claude connects to them from Anthropic's servers, and members sign in with their own accounts where needed. |
245245| Roles > connector permissions in custom roles (Enterprise) | Partially supported in Claude Science | Apply to the connectors on your **Connectors** page, which the app reaches through Anthropic. They don't apply to the Featured connectors that run on members' computers or to custom connectors members add in the Claude Science app. The **Claude Science** page controls those Featured connectors for every member. The **Allow custom connectors** switch there decides whether members can add and use custom connectors, and a separate capability in custom roles, **Custom connectors**, can limit that to certain roles (see [Capabilities in custom roles](#capabilities-in-custom-roles)). |
246| Plugins > plugins you add for the organization | Partially supported in Claude Science | Plugins you set to **Installed by default** or **Required** are synced to members' Claude Science app, which loads their skills and connectors. Plugins left as **Available to install** aren't offered in the app, and plugin commands don't apply there. Which Featured connectors and skills members can use, and whether they can add their own, are separate controls on the **Claude Science** page (see [Featured connectors and skills](#featured-connectors-and-skills), [Custom connectors](#custom-connectors), and [Custom skills](#custom-skills)). |
246| Plugins > plugins you add for the organization | Partially supported in Claude Science | Plugins you set to **Installed by default** or **Required** are synced to members' Claude Science app, which loads their skills and connectors. A plugin's connector prompts each member for approval per tool, and its interactive output doesn't open in the app. Plugins left as **Available to install** aren't offered in the app, and plugin commands don't apply there. Which Featured connectors and skills members can use, and whether they can add their own, are separate controls on the **Claude Science** page (see [Featured connectors and skills](#featured-connectors-and-skills), [Custom connectors](#custom-connectors), and [Custom skills](#custom-skills)). |
247247| Connectors > Tunnels API (Enterprise) | Partially supported in Claude Science | A connector your organization serves through a tunnel works in the app the same way it does in claude.ai, because the app reaches the connectors on your **Connectors** page through Anthropic's hosted connector service. Custom connectors a member adds in the Claude Science app connect directly from the member's computer and never use a tunnel (admins can restrict this in [Custom connectors](#custom-connectors)). |
248248| Connectors > connectors members add themselves | Supported in Claude Science | In claude.ai, members use only the connectors on your **Connectors** page. In Claude Science, members can also add custom connectors (a server URL or a local command) while the **Allow custom connectors** switch is on, which it is by default for Team and not for Enterprise, and the **Connectors** page and its restrictions don't apply to those. Turn off the **Allow custom connectors** switch under **Organization settings** > **Claude Science** to limit members to Featured connectors and the connectors you add on your **Connectors** page (see [Custom connectors](#custom-connectors)). On Enterprise plans, you can also leave the switch on and limit custom connectors to certain custom roles (see [Capabilities in custom roles](#capabilities-in-custom-roles)). |
249249| Connectors > Desktop extension allowlist | Not applicable in Claude Science | Claude Science doesn't install desktop extensions, so there is nothing for this setting to govern. |
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3535
3636## Using connectors
3737
38Name a source in your request, or describe what you need and Claude chooses from available connector tools. Connector queries appear in the conversation as expandable code steps. Featured connectors you've previously enabled run without a permission card. Connectors you add yourself prompt for approval per tool, with Once, This conversation, This project, or Global scope.
38Name a source in your request, or describe what you need and Claude chooses from available connector tools. Connector queries appear in the conversation as expandable code steps. Featured connectors you've previously enabled run without a permission card. Connectors you add yourself, and connectors that your organization's plugins add, prompt for approval per tool, with Once, This conversation, This project, or Global scope.
3939
4040The databases behind Featured connectors are on the network allowlist in groups under Settings > Network. Turning off a group disables the connectors that depend on it.
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1717
1818## How Claude responds to findings
1919
20If the reviewer finds something, each finding appears as a card directly under the message it refers to, showing what the reviewer found and the finding's status. A message with more than three findings shows the first three and a **Show all** control. Click a card to open the reviewer's full reasoning. Claude reads the findings and addresses them in its next message, either by correcting the work or by explaining why the finding doesn't apply.
20If the reviewer finds something, each finding appears as a card directly under the message it refers to, showing what the reviewer found and the finding's status. A message with more than three findings shows the first three and a **Show all** control. Click a card to open it in place and read the reviewer's reason, and select the **View reviewer transcript** button on the open card for the reviewer's full transcript. Claude reads the findings and addresses them in its next message, either by correcting the work or by explaining why the finding doesn't apply.
2121
2222## Adding your own review criteria
2323