docs: fix step numbering in README#343
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Thanks for the feedback! I’ve updated the PR to keep only the step numbering fix and removed the additional documentation changes. |
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Actionable comments posted: 5
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@README.md`:
- Line 76: Update README to consistently use Docker Compose v2 syntax: replace
all occurrences of the legacy "docker-compose" command (e.g., the
"docker-compose up -d --build" invocation) with the recommended "docker compose"
form so examples like "docker compose up -d --build" and "docker compose ps" use
the same binary; ensure both occurrences mentioned (the up command and the ps
command) are standardized and any related instructions or examples are updated
to match Compose v2.
- Around line 90-94: The docker run snippet is unclear and mismatched with the
text; update the README so the command is either removed OR clearly presented as
an alternative to docker-compose (e.g., "As an alternative to docker-compose,
run the container directly: docker run -p 8505:8501 openms_streamlit_template")
and fix the explanatory text to state that the host port 8505 is mapped to the
container's default Streamlit port 8501 (or change the command to docker run -p
8501:8501 if you intend the host to also be 8501); ensure the sentence
referencing the port reflects the chosen mapping and that the docker run example
is placed with explicit context.
- Line 79: The README has three fenced code blocks missing language tags
(violates MD040) — update the three backticks enclosing the docker-compose
output containing "[+] Running 2/2" to use a text/console tag (e.g. ```text),
the docker compose ps table starting with "CONTAINER ID IMAGE ..." to use
```text, and the docker run command "docker run -p 8505:8501
openms_streamlit_template" to use ```bash so syntax highlighting is enabled and
markdownlint MD040 is satisfied.
- Line 70: Change the product name capitalization in the README sentence "Create
a temporary `.env` file with your Github token." to use the official casing
"GitHub" (capital H); locate the exact string in the README and replace "Github"
with "GitHub" so the sentence reads "Create a temporary `.env` file with your
GitHub token."
- Around line 50-68: The README mixes two descriptive list items (`Dockerfile`
and `Dockerfile_simple`) with the actual Docker setup steps, so the ordered
numbering for "Install Docker", "Test Docker", and "Clone the repository"
continues from 3 instead of restarting at 1; fix this by separating the two
Dockerfile descriptions from the setup steps (e.g., move `Dockerfile` and
`Dockerfile_simple` into their own paragraph or a bulleted list) and then start
a new ordered list for the setup steps beginning with "Install Docker", "Test
Docker", and "Clone the repository" so those headings render as steps 1, 2, 3.
| cd streamlit-template | ||
| ``` | ||
| 6. **Specify GitHub token (to download Windows executables).** | ||
| Create a temporary `.env` file with your Github token. |
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"Github" should be "GitHub" (capital H)
The official product name uses a capital H. Flagged by LanguageTool.
📝 Proposed fix
- Create a temporary `.env` file with your Github token.
+ Create a temporary `.env` file with your GitHub token.📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| Create a temporary `.env` file with your Github token. | |
| Create a temporary `.env` file with your GitHub token. |
🧰 Tools
🪛 LanguageTool
[uncategorized] ~70-~70: The official name of this software platform is spelled with a capital “H”.
Context: ...reate a temporary .env file with your Github token. It should contain only one lin...
(GITHUB)
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@README.md` at line 70, Change the product name capitalization in the README
sentence "Create a temporary `.env` file with your Github token." to use the
official casing "GitHub" (capital H); locate the exact string in the README and
replace "Github" with "GitHub" so the sentence reads "Create a temporary `.env`
file with your GitHub token."
| 7. **Build & Launch the App** | ||
| To build and start the containers. From the project root directory: | ||
| ```bash | ||
| docker-compose up -d --build |
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Inconsistent docker-compose vs docker compose command syntax
Line 76 uses docker-compose up -d --build (Compose v1 standalone binary) while line 84 uses docker compose ps (Compose v2 plugin syntax). These are different binaries and may not both be available on the same system. Pick one consistently — Compose v2 (docker compose) is the current recommended form.
📝 Proposed fix (standardise on Compose v2)
- docker-compose up -d --build
+ docker compose up -d --buildAlso applies to: 84-84
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@README.md` at line 76, Update README to consistently use Docker Compose v2
syntax: replace all occurrences of the legacy "docker-compose" command (e.g.,
the "docker-compose up -d --build" invocation) with the recommended "docker
compose" form so examples like "docker compose up -d --build" and "docker
compose ps" use the same binary; ensure both occurrences mentioned (the up
command and the ps command) are standardized and any related instructions or
examples are updated to match Compose v2.
| docker-compose up -d --build | ||
| ``` | ||
| At the end, you should see this: | ||
| ``` |
There was a problem hiding this comment.
Fenced code blocks are missing language specifiers
Three code blocks have no language tag, which violates markdownlint rule MD040 and degrades syntax-highlighting in rendered documentation.
📝 Proposed fix
Line 79 (docker-compose output — use text or console):
- ```
+ ```text
[+] Running 2/2Line 85 (docker compose ps table — use text):
- ```
+ ```text
CONTAINER ID IMAGE ...Line 91 (docker run command — use bash):
- ```
+ ```bash
docker run -p 8505:8501 openms_streamlit_templateAlso applies to: 85-85, 91-91
🧰 Tools
🪛 markdownlint-cli2 (0.21.0)
[warning] 79-79: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@README.md` at line 79, The README has three fenced code blocks missing
language tags (violates MD040) — update the three backticks enclosing the
docker-compose output containing "[+] Running 2/2" to use a text/console tag
(e.g. ```text), the docker compose ps table starting with "CONTAINER ID IMAGE
..." to use ```text, and the docker run command "docker run -p 8505:8501
openms_streamlit_template" to use ```bash so syntax highlighting is enabled and
markdownlint MD040 is satisfied.
| To map the port to default streamlit port `8501` and launch. | ||
| ``` | ||
| docker run -p 8505:8501 openms_streamlit_template | ||
|
|
||
| ``` |
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The trailing docker run command is disconnected and potentially confusing
After a complete docker-compose workflow (build, start, verify with docker compose ps), line 90 introduces docker run -p 8505:8501 openms_streamlit_template without explanation of when or why to use it. Additionally, the accompanying text says "map the port to default streamlit port 8501" yet the external port is 8505, not 8501 — which is likely to confuse readers. If this command is intended as an alternative to docker-compose, that context should be made explicit; otherwise, consider removing it.
🧰 Tools
🪛 markdownlint-cli2 (0.21.0)
[warning] 91-91: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@README.md` around lines 90 - 94, The docker run snippet is unclear and
mismatched with the text; update the README so the command is either removed OR
clearly presented as an alternative to docker-compose (e.g., "As an alternative
to docker-compose, run the container directly: docker run -p 8505:8501
openms_streamlit_template") and fix the explanatory text to state that the host
port 8505 is mapped to the container's default Streamlit port 8501 (or change
the command to docker run -p 8501:8501 if you intend the host to also be 8501);
ensure the sentence referencing the port reflects the chosen mapping and that
the docker run example is placed with explicit context.
There was a problem hiding this comment.
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Duplicate comments:
In `@README.md`:
- Line 75: The README contains the incorrect casing "Github" in the sentence
"Create a temporary `.env` file with your Github token"; update that string to
"GitHub" (capital G and H) so it reads "Create a temporary `.env` file with your
GitHub token" — locate the occurrence of "Github" in the README content and
replace it with "GitHub".
- Around line 81-101: Choose a consistent Docker CLI form and update the README
to use it everywhere (replace either "docker-compose up -d --build" or "docker
compose ps" so both use the same binary; prefer "docker compose" for Docker v2)
and add language specifiers to all fenced code blocks shown (e.g., add "bash"
after the opening backticks for the blocks containing "docker compose up -d
--build", the container status output, and "docker run -p 8505:8501
openms_streamlit_template") so markdownlint MD040 is satisfied.
- Around line 50-73: The numbered list currently mixes the Dockerfile
descriptions with the installation steps so "Install Docker" appears as step 3;
convert the first two numbered items ("Dockerfile" and "Dockerfile_simple"
descriptions) into an unordered list or a short paragraph (leave their text
as-is) and then start a new ordered list for the setup steps beginning with
"Install Docker" (the items "Install Docker", "Test Docker", "Clone the
repository", etc.) so numbering restarts at 1; update the README.md list markers
accordingly to ensure the setup guide is its own numbered sequence.
- Around line 97-101: The README's docker instruction text is inconsistent and
misleading: either update the command or the explanatory text and clarify
context. Change the sentence "map the port to default streamlit port `8501`" to
explicitly state "maps host port 8505 to container port 8501" if you keep the
command `docker run -p 8505:8501 openms_streamlit_template`, or change the
command to `docker run -p 8501:8501 openms_streamlit_template` to match the
original wording; also add a brief note after the docker run line explaining
this is an alternative to the docker-compose workflow and when to use the
standalone `docker run` (e.g., quick local test vs full compose stack).
2 participants
Fixes incorrect step numbering in the Docker setup section of README.md.
Only numbering was updated (no other documentation changes), as requested in the issue discussion.
Related to: #174
Summary by CodeRabbit