alcedo-lit 0.1.0__tar.gz

alcedo_lit-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Alcedo contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

alcedo_lit-0.1.0/PKG-INFO

@@ -0,0 +1,225 @@
+Metadata-Version: 2.4
+Name: alcedo-lit
+Version: 0.1.0
+Summary: Collect DOIs from a list of literature search queries, grouped by query.
+Author: Alcedo contributors
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/Prostochell-544/Alcedo
+Project-URL: Issues, https://github.com/Prostochell-544/Alcedo/issues
+Project-URL: Changelog, https://github.com/Prostochell-544/Alcedo/blob/main/CHANGELOG.md
+Keywords: literature search,doi,bibliometrics,systematic review,openalex,semantic scholar,google scholar
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: THIRD_PARTY_NOTICES.md
+Requires-Dist: requests>=2.31
+Requires-Dist: tqdm>=4.66
+Provides-Extra: scholar
+Requires-Dist: scholarly>=1.7.11; extra == "scholar"
+Requires-Dist: bibtexparser<2; extra == "scholar"
+Requires-Dist: httpx<0.28; extra == "scholar"
+Provides-Extra: dev
+Requires-Dist: pytest>=8; extra == "dev"
+Requires-Dist: ruff>=0.6; extra == "dev"
+Dynamic: license-file
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Prostochell-544/Alcedo/main/docs/assets/alcedo-logo.png" alt="Alcedo logo: a kingfisher in flight" width="220">
+  <br>
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/Prostochell-544/Alcedo/main/docs/assets/alcedo-wordmark-dark.svg">
+    <img src="https://raw.githubusercontent.com/Prostochell-544/Alcedo/main/docs/assets/alcedo-wordmark-light.svg" alt="Alcedo: open metadata extractor" width="320">
+  </picture>
+</p>
+
+# Alcedo
+
+*Alcedo* is the Latin name of the kingfisher, which dives and picks out exactly what it wants.
+
+Alcedo turns a list of literature search queries into DOIs grouped by query. Put your
+boolean queries in a file and run one command. The results are a text file with one
+block per query. There is no export to reference managers yet.
+
+**Status: alpha.** Options may change. See the [roadmap](https://github.com/Prostochell-544/Alcedo/blob/main/docs/ROADMAP.md) and the [changelog](https://github.com/Prostochell-544/Alcedo/blob/main/CHANGELOG.md).
+Documentation in other languages: [Russian](https://github.com/Prostochell-544/Alcedo/blob/main/docs/ru/query-rules.md), [Ukrainian](https://github.com/Prostochell-544/Alcedo/blob/main/docs/uk/query-rules.md).
+
+## What it does
+
+- Takes up to 5 result pages (50 results) per query, or all of them if there are fewer.
+- Searches Google Scholar through a search API with your own key. Without a working API it uses Semantic Scholar and
+  OpenAlex, plus direct Google Scholar search if you turned that on. See [Which source to use](#which-source-to-use).
+- A source that fails is left out, and the block says so.
+- Scholar gives links rather than DOIs, so Alcedo looks for the DOI in the URL, Europe PMC and
+  publisher meta tags, then by title in Crossref and OpenAlex.
+- Saves after every query. `--resume` continues after an interruption and collects failed queries again.
+- Writes a second file listing each DOI once, with the queries that found it. Papers found by the most queries come first.
+- With `--verify-dois`, checks every DOI in the doi.org registry and marks the ones that do not exist.
+
+## Install
+
+Requires Python 3.10 or newer.
+
+```bash
+pip install alcedo-lit
+```
+
+For direct Google Scholar search, which most people will not need, install the extra as well:
+`pip install "alcedo-lit[scholar]"`.
+
+Then choose how to search. This explains the options and saves your key, which is not shown as you type:
+
+```bash
+alcedo setup
+```
+
+## Quick start
+
+The repository includes a sample: [queries.txt](https://github.com/Prostochell-544/Alcedo/blob/main/queries.txt) has two queries about the kingfisher, and
+[alcedo_results.txt](https://github.com/Prostochell-544/Alcedo/blob/main/alcedo_results.txt) and [alcedo_results_unique.csv](https://github.com/Prostochell-544/Alcedo/blob/main/alcedo_results_unique.csv) are their
+results. There is another set of queries in [examples/queries.txt](https://github.com/Prostochell-544/Alcedo/blob/main/examples/queries.txt).
+
+For your own search, create a `queries.txt` in any folder, with `;` after each query:
+
+```text
+biomimetic nacre ("brick-and-mortar" OR "layered structure") composite fracture toughness;
+gecko-inspired dry adhesive (micropillar OR "hierarchical microstructure") adhesion;
+```
+
+From that folder, check the queries for common mistakes and then run them:
+
+```bash
+alcedo check
+alcedo
+```
+
+The results go to `alcedo_results.txt` in the current folder:
+
+```text
+=== Query: gecko-inspired dry adhesive (micropillar OR "hierarchical microstructure") adhesion ===
+Source: OpenAlex
+https://doi.org/10.1039/c3sm52921e
+https://doi.org/10.1098/rsif.2018.0681
+```
+
+The `Source:` line appears when the results did not all come from a search API. Records with no DOI are
+listed as `DOI not found: <title>`, and a query that failed has a `Query error` line. If DOI
+lookups failed along the way, the final message says how many, because those records may still have a DOI.
+
+Alcedo will not replace an existing results file: use `--resume` to continue it or `--overwrite` to start again.
+
+`alcedo_results_unique.csv` lists each DOI once, with the number of queries that found it and the queries themselves.
+It is built from the results file and uses no extra searches. Cells are separated by `;`, which Excel in European
+locales expects.
+
+To check DOIs against the doi.org registry, add `--verify-dois`. This also works on results you already have:
+`alcedo --resume --verify-dois`. A DOI the registry does not know becomes `DOI not registered: <doi>`, and one that
+could not be checked stays in the results and is counted in the final message. The check uses no OpenAlex budget.
+
+To check the wording of a query quickly, look at its first 10 results:
+
+```bash
+alcedo --pages 1 -i test.txt -o test_results.txt --overwrite
+```
+
+Read [how to write queries](https://github.com/Prostochell-544/Alcedo/blob/main/docs/query-syntax.md) before a large run. Some mistakes fail silently: a lowercase
+`or`, for example, is treated as AND. `alcedo check` finds the common ones.
+
+## Which source to use
+
+With a working API key, a query uses only the API. Otherwise it uses the free sources together, in this order:
+Semantic Scholar, OpenAlex, and direct search if you turned it on. Each gives up to 50 results and repeats are
+removed, so a block can hold more than 50 records. A source that fails is left out, and the `Source:` line says so.
+If every source fails, the block has a `Query error` line and `--resume` collects it again.
+
+The free options do not give the same results as an API. The figures below come from small tests with relevance
+judged by an AI assistant, not by a domain expert. Treat them as a rough guide. Results vary a lot by query.
+
+| Source | What you need | Cost at the time of writing | How it did |
+|---|---|---|---|
+| Google Scholar via [SearchApi](https://www.searchapi.io) | Your key, no phone number | 100 free requests to try it, then from $40 a month | Best first results: 13 of the first 20 were exactly on topic. Same first results as a browser in our check |
+| Google Scholar via [Serper](https://serper.dev) | Your key, no card | 2,500 free queries, which is about 500 queries of 50 results, then one-off packs from $50 for 50,000, valid for 6 months | Same first 10 results as SearchApi on both test queries, and 13 of the first 20 exactly on topic. Later results differed |
+| Google Scholar via [SerpApi](https://serpapi.com) | Your key and a phone number | 250 free searches a month, paid plans from $25 a month | Not measured; Alcedo has not yet been run against the live service |
+| [Semantic Scholar](https://www.semanticscholar.org/product/api) | Nothing; a free key gives you your own limit | Free | 9 of the first 10 exactly on topic on one query, no results on a stricter one. Finds few but precise papers, most cited first. Not measured inside Alcedo |
+| OpenAlex | Nothing; a [free key](https://openalex.org/settings/api) raises the daily budget | Free | 5 of the first 20 exactly on topic. Its share of on-topic results ranged from 34% against 73% for the API to about equal. It also found papers Scholar missed |
+| Google Scholar directly | `pip install "alcedo-lit[scholar]"` and your agreement | Free | Changes a lot between runs and networks, see below |
+
+A query with 50 results uses 3 requests on SearchApi and 5 on Serper. You create the key and accept the provider's terms, and the
+provider sees your queries. If you have neither a key nor a budget for one, the free catalogues still work, and direct
+search can add to them on a network Scholar accepts.
+
+In a run where Scholar answered in full, the free sources together found 38 of the 45 exactly on-topic papers known
+from all our runs, against 29 for SearchApi. Their first results were weaker, with 9 of the first 20 exactly on topic
+against 13, and they took 15 minutes for 2 queries against 3.5, mostly on direct search and DOI lookups. A key gives you
+the best first results quickly, but going without one does not have to mean missing papers.
+
+Publications that use results from Semantic Scholar should cite the Semantic Scholar Open Data Platform, as its
+[API license](https://www.semanticscholar.org/product/api/license) asks.
+
+### Direct search
+
+It is free, and Scholar may simply refuse it. Scholar often refuses VPNs and shared networks: in our test, one VPN
+provider was refused even in a browser and another was accepted. If it refuses you, try without the VPN, and check
+the same search in a browser.
+
+**An answer from Scholar does not mean the list is complete.** In some of our tests, the script got 6 to 27 results
+for queries that give 50 through an API, mostly recent papers, with key works missing, and repeating one query gave
+different lists. In a later run it got all 50, nearly all of them also in the API's list. Parsing does not explain the
+difference, we do not know the cause, and you cannot tell in advance which you will get. So Alcedo puts direct results after the free catalogues,
+where they can only add to the list, and marks those blocks in the results file. Do not rely on direct search for a
+literature review. If you add a key later, `alcedo --redo-free` collects those blocks again.
+
+Alcedo asks once before using direct search, and remembers your answer. `alcedo setup` changes it, and
+`--direct-scholar` or `--no-direct-scholar` overrides it for one run.
+
+### Keys and everyday commands
+
+`alcedo setup` stores keys as plain text in your user settings (`%APPDATA%\alcedo\config.json` on Windows,
+`~/.config/alcedo/config.json` elsewhere). Run it again and type `-` to remove a key. The `SEARCHAPI_KEY`,
+`SERPER_API_KEY`, `SERPAPI_KEY`, `OPENALEX_API_KEY` and `SEMANTIC_SCHOLAR_API_KEY` environment variables take priority
+over that file, and command line options take priority over both.
+
+```bash
+alcedo --resume          # continue after an interruption
+alcedo --redo-free   # collect blocks from the free sources again, for example after adding a key
+alcedo --source openalex # OpenAlex only
+alcedo --no-semantic-scholar  # leave Semantic Scholar out of the free sources
+alcedo --help            # all options
+```
+
+## Responsible use
+
+- Direct Google Scholar search is off until you agree to it. Scholar's `robots.txt` disallows automated search, and
+  you are responsible for following Google's terms. Alcedo waits between queries and stops asking when Scholar
+  refuses. The `scholarly` library it relies on sends a random browser User-Agent and may try to open a browser for
+  a captcha, and it has no setting to turn that off.
+- Apart from that route, requests identify themselves as `alcedo/<version>`. With `--mailto`, your
+  address goes to Crossref, OpenAlex, Semantic Scholar and Europe PMC, never to publisher sites.
+- Alcedo collects metadata. It does not download papers and will not integrate shadow libraries.
+
+## Development
+
+```bash
+pip install -e ".[dev]"
+python -m pytest
+ruff check .
+```
+
+The tests use no network. Git tracks the sample in the project root, so do not run your own queries there:
+`queries.txt`, `alcedo_results.txt` and `alcedo_results_unique.csv` would show up as changes. Use `private/`, which
+Git ignores, so your topic stays out of the repository.
+
+## License
+
+The code is under the [MIT](https://github.com/Prostochell-544/Alcedo/blob/main/LICENSE) license. The logo is not: see the [third-party notices](https://github.com/Prostochell-544/Alcedo/blob/main/THIRD_PARTY_NOTICES.md).
+
+## Special thanks
+
+To [kesha_xdd](https://t.me/kesha_xdd), who drew the Alcedo logo.

alcedo_lit-0.1.0/README.md

@@ -0,0 +1,192 @@
+<p align="center">
+  <img src="https://raw.githubusercontent.com/Prostochell-544/Alcedo/main/docs/assets/alcedo-logo.png" alt="Alcedo logo: a kingfisher in flight" width="220">
+  <br>
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/Prostochell-544/Alcedo/main/docs/assets/alcedo-wordmark-dark.svg">
+    <img src="https://raw.githubusercontent.com/Prostochell-544/Alcedo/main/docs/assets/alcedo-wordmark-light.svg" alt="Alcedo: open metadata extractor" width="320">
+  </picture>
+</p>
+
+# Alcedo
+
+*Alcedo* is the Latin name of the kingfisher, which dives and picks out exactly what it wants.
+
+Alcedo turns a list of literature search queries into DOIs grouped by query. Put your
+boolean queries in a file and run one command. The results are a text file with one
+block per query. There is no export to reference managers yet.
+
+**Status: alpha.** Options may change. See the [roadmap](https://github.com/Prostochell-544/Alcedo/blob/main/docs/ROADMAP.md) and the [changelog](https://github.com/Prostochell-544/Alcedo/blob/main/CHANGELOG.md).
+Documentation in other languages: [Russian](https://github.com/Prostochell-544/Alcedo/blob/main/docs/ru/query-rules.md), [Ukrainian](https://github.com/Prostochell-544/Alcedo/blob/main/docs/uk/query-rules.md).
+
+## What it does
+
+- Takes up to 5 result pages (50 results) per query, or all of them if there are fewer.
+- Searches Google Scholar through a search API with your own key. Without a working API it uses Semantic Scholar and
+  OpenAlex, plus direct Google Scholar search if you turned that on. See [Which source to use](#which-source-to-use).
+- A source that fails is left out, and the block says so.
+- Scholar gives links rather than DOIs, so Alcedo looks for the DOI in the URL, Europe PMC and
+  publisher meta tags, then by title in Crossref and OpenAlex.
+- Saves after every query. `--resume` continues after an interruption and collects failed queries again.
+- Writes a second file listing each DOI once, with the queries that found it. Papers found by the most queries come first.
+- With `--verify-dois`, checks every DOI in the doi.org registry and marks the ones that do not exist.
+
+## Install
+
+Requires Python 3.10 or newer.
+
+```bash
+pip install alcedo-lit
+```
+
+For direct Google Scholar search, which most people will not need, install the extra as well:
+`pip install "alcedo-lit[scholar]"`.
+
+Then choose how to search. This explains the options and saves your key, which is not shown as you type:
+
+```bash
+alcedo setup
+```
+
+## Quick start
+
+The repository includes a sample: [queries.txt](https://github.com/Prostochell-544/Alcedo/blob/main/queries.txt) has two queries about the kingfisher, and
+[alcedo_results.txt](https://github.com/Prostochell-544/Alcedo/blob/main/alcedo_results.txt) and [alcedo_results_unique.csv](https://github.com/Prostochell-544/Alcedo/blob/main/alcedo_results_unique.csv) are their
+results. There is another set of queries in [examples/queries.txt](https://github.com/Prostochell-544/Alcedo/blob/main/examples/queries.txt).
+
+For your own search, create a `queries.txt` in any folder, with `;` after each query:
+
+```text
+biomimetic nacre ("brick-and-mortar" OR "layered structure") composite fracture toughness;
+gecko-inspired dry adhesive (micropillar OR "hierarchical microstructure") adhesion;
+```
+
+From that folder, check the queries for common mistakes and then run them:
+
+```bash
+alcedo check
+alcedo
+```
+
+The results go to `alcedo_results.txt` in the current folder:
+
+```text
+=== Query: gecko-inspired dry adhesive (micropillar OR "hierarchical microstructure") adhesion ===
+Source: OpenAlex
+https://doi.org/10.1039/c3sm52921e
+https://doi.org/10.1098/rsif.2018.0681
+```
+
+The `Source:` line appears when the results did not all come from a search API. Records with no DOI are
+listed as `DOI not found: <title>`, and a query that failed has a `Query error` line. If DOI
+lookups failed along the way, the final message says how many, because those records may still have a DOI.
+
+Alcedo will not replace an existing results file: use `--resume` to continue it or `--overwrite` to start again.
+
+`alcedo_results_unique.csv` lists each DOI once, with the number of queries that found it and the queries themselves.
+It is built from the results file and uses no extra searches. Cells are separated by `;`, which Excel in European
+locales expects.
+
+To check DOIs against the doi.org registry, add `--verify-dois`. This also works on results you already have:
+`alcedo --resume --verify-dois`. A DOI the registry does not know becomes `DOI not registered: <doi>`, and one that
+could not be checked stays in the results and is counted in the final message. The check uses no OpenAlex budget.
+
+To check the wording of a query quickly, look at its first 10 results:
+
+```bash
+alcedo --pages 1 -i test.txt -o test_results.txt --overwrite
+```
+
+Read [how to write queries](https://github.com/Prostochell-544/Alcedo/blob/main/docs/query-syntax.md) before a large run. Some mistakes fail silently: a lowercase
+`or`, for example, is treated as AND. `alcedo check` finds the common ones.
+
+## Which source to use
+
+With a working API key, a query uses only the API. Otherwise it uses the free sources together, in this order:
+Semantic Scholar, OpenAlex, and direct search if you turned it on. Each gives up to 50 results and repeats are
+removed, so a block can hold more than 50 records. A source that fails is left out, and the `Source:` line says so.
+If every source fails, the block has a `Query error` line and `--resume` collects it again.
+
+The free options do not give the same results as an API. The figures below come from small tests with relevance
+judged by an AI assistant, not by a domain expert. Treat them as a rough guide. Results vary a lot by query.
+
+| Source | What you need | Cost at the time of writing | How it did |
+|---|---|---|---|
+| Google Scholar via [SearchApi](https://www.searchapi.io) | Your key, no phone number | 100 free requests to try it, then from $40 a month | Best first results: 13 of the first 20 were exactly on topic. Same first results as a browser in our check |
+| Google Scholar via [Serper](https://serper.dev) | Your key, no card | 2,500 free queries, which is about 500 queries of 50 results, then one-off packs from $50 for 50,000, valid for 6 months | Same first 10 results as SearchApi on both test queries, and 13 of the first 20 exactly on topic. Later results differed |
+| Google Scholar via [SerpApi](https://serpapi.com) | Your key and a phone number | 250 free searches a month, paid plans from $25 a month | Not measured; Alcedo has not yet been run against the live service |
+| [Semantic Scholar](https://www.semanticscholar.org/product/api) | Nothing; a free key gives you your own limit | Free | 9 of the first 10 exactly on topic on one query, no results on a stricter one. Finds few but precise papers, most cited first. Not measured inside Alcedo |
+| OpenAlex | Nothing; a [free key](https://openalex.org/settings/api) raises the daily budget | Free | 5 of the first 20 exactly on topic. Its share of on-topic results ranged from 34% against 73% for the API to about equal. It also found papers Scholar missed |
+| Google Scholar directly | `pip install "alcedo-lit[scholar]"` and your agreement | Free | Changes a lot between runs and networks, see below |
+
+A query with 50 results uses 3 requests on SearchApi and 5 on Serper. You create the key and accept the provider's terms, and the
+provider sees your queries. If you have neither a key nor a budget for one, the free catalogues still work, and direct
+search can add to them on a network Scholar accepts.
+
+In a run where Scholar answered in full, the free sources together found 38 of the 45 exactly on-topic papers known
+from all our runs, against 29 for SearchApi. Their first results were weaker, with 9 of the first 20 exactly on topic
+against 13, and they took 15 minutes for 2 queries against 3.5, mostly on direct search and DOI lookups. A key gives you
+the best first results quickly, but going without one does not have to mean missing papers.
+
+Publications that use results from Semantic Scholar should cite the Semantic Scholar Open Data Platform, as its
+[API license](https://www.semanticscholar.org/product/api/license) asks.
+
+### Direct search
+
+It is free, and Scholar may simply refuse it. Scholar often refuses VPNs and shared networks: in our test, one VPN
+provider was refused even in a browser and another was accepted. If it refuses you, try without the VPN, and check
+the same search in a browser.
+
+**An answer from Scholar does not mean the list is complete.** In some of our tests, the script got 6 to 27 results
+for queries that give 50 through an API, mostly recent papers, with key works missing, and repeating one query gave
+different lists. In a later run it got all 50, nearly all of them also in the API's list. Parsing does not explain the
+difference, we do not know the cause, and you cannot tell in advance which you will get. So Alcedo puts direct results after the free catalogues,
+where they can only add to the list, and marks those blocks in the results file. Do not rely on direct search for a
+literature review. If you add a key later, `alcedo --redo-free` collects those blocks again.
+
+Alcedo asks once before using direct search, and remembers your answer. `alcedo setup` changes it, and
+`--direct-scholar` or `--no-direct-scholar` overrides it for one run.
+
+### Keys and everyday commands
+
+`alcedo setup` stores keys as plain text in your user settings (`%APPDATA%\alcedo\config.json` on Windows,
+`~/.config/alcedo/config.json` elsewhere). Run it again and type `-` to remove a key. The `SEARCHAPI_KEY`,
+`SERPER_API_KEY`, `SERPAPI_KEY`, `OPENALEX_API_KEY` and `SEMANTIC_SCHOLAR_API_KEY` environment variables take priority
+over that file, and command line options take priority over both.
+
+```bash
+alcedo --resume          # continue after an interruption
+alcedo --redo-free   # collect blocks from the free sources again, for example after adding a key
+alcedo --source openalex # OpenAlex only
+alcedo --no-semantic-scholar  # leave Semantic Scholar out of the free sources
+alcedo --help            # all options
+```
+
+## Responsible use
+
+- Direct Google Scholar search is off until you agree to it. Scholar's `robots.txt` disallows automated search, and
+  you are responsible for following Google's terms. Alcedo waits between queries and stops asking when Scholar
+  refuses. The `scholarly` library it relies on sends a random browser User-Agent and may try to open a browser for
+  a captcha, and it has no setting to turn that off.
+- Apart from that route, requests identify themselves as `alcedo/<version>`. With `--mailto`, your
+  address goes to Crossref, OpenAlex, Semantic Scholar and Europe PMC, never to publisher sites.
+- Alcedo collects metadata. It does not download papers and will not integrate shadow libraries.
+
+## Development
+
+```bash
+pip install -e ".[dev]"
+python -m pytest
+ruff check .
+```
+
+The tests use no network. Git tracks the sample in the project root, so do not run your own queries there:
+`queries.txt`, `alcedo_results.txt` and `alcedo_results_unique.csv` would show up as changes. Use `private/`, which
+Git ignores, so your topic stays out of the repository.
+
+## License
+
+The code is under the [MIT](https://github.com/Prostochell-544/Alcedo/blob/main/LICENSE) license. The logo is not: see the [third-party notices](https://github.com/Prostochell-544/Alcedo/blob/main/THIRD_PARTY_NOTICES.md).
+
+## Special thanks
+
+To [kesha_xdd](https://t.me/kesha_xdd), who drew the Alcedo logo.

alcedo_lit-0.1.0/THIRD_PARTY_NOTICES.md

@@ -0,0 +1,36 @@
+# Third-party notices
+
+Alcedo contains no code copied from other projects so far.
+
+If you copy code from another project, add an entry here with the project name, its
+URL, the files concerned and the full text of its license and copyright notice. Keep
+any notices from the original source. Apache-2.0 projects may also have a NOTICE file
+that has to be preserved.
+
+Projects whose ideas informed Alcedo's design are listed in `docs/ROADMAP.md`.
+
+## Logo
+
+`docs/assets/alcedo-logo.png` was drawn by [kesha_xdd](https://t.me/kesha_xdd). All rights stay with the artist, who
+allowed its use for this project. It is not covered by the MIT license of the code, so forks and other projects need
+the artist's own permission to use it.
+
+## Wordmark
+
+`docs/assets/alcedo-wordmark-light.svg` and `alcedo-wordmark-dark.svg` show text set in Orbitron and converted to
+outlines. The repository does not contain the font itself.
+
+Orbitron: Copyright 2018 The Orbitron Project Authors (https://github.com/theleagueof/orbitron), with Reserved Font
+Name "Orbitron". Licensed under the SIL Open Font License, Version 1.1: https://openfontlicense.org
+
+## Runtime dependencies
+
+These are installed separately and are not distributed with Alcedo.
+
+| Package | License | Needed for |
+|---|---|---|
+| requests | Apache-2.0 | always |
+| tqdm | MPL-2.0 AND MIT | always |
+| scholarly | Unlicense | optional `scholar` extra |
+| bibtexparser | LGPLv3 or BSD (version 1.x) | optional `scholar` extra |
+| httpx | BSD-3-Clause | optional `scholar` extra |

alcedo_lit-0.1.0/pyproject.toml

@@ -0,0 +1,66 @@
+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "alcedo-lit"
+dynamic = ["version"]
+description = "Collect DOIs from a list of literature search queries, grouped by query."
+readme = "README.md"
+requires-python = ">=3.10"
+license = "MIT"
+license-files = ["LICENSE", "THIRD_PARTY_NOTICES.md"]
+authors = [{ name = "Alcedo contributors" }]
+keywords = ["literature search", "doi", "bibliometrics", "systematic review", "openalex", "semantic scholar",
+            "google scholar"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering",
+]
+dependencies = [
+    "requests>=2.31",
+    "tqdm>=4.66",
+]
+
+[project.urls]
+Homepage = "https://github.com/Prostochell-544/Alcedo"
+Issues = "https://github.com/Prostochell-544/Alcedo/issues"
+Changelog = "https://github.com/Prostochell-544/Alcedo/blob/main/CHANGELOG.md"
+
+[project.optional-dependencies]
+# Direct Google Scholar access. scholarly 1.7.11 imports a module that
+# bibtexparser 2 removed, and passes an argument to httpx.Client that httpx 0.28 removed.
+scholar = [
+    "scholarly>=1.7.11",
+    "bibtexparser<2",
+    "httpx<0.28",
+]
+dev = [
+    "pytest>=8",
+    "ruff>=0.6",
+]
+
+[project.scripts]
+alcedo = "alcedo_lit.cli:main"
+
+[tool.setuptools.dynamic]
+version = { attr = "alcedo_lit.__version__" }
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.ruff]
+line-length = 120
+src = ["src", "tests"]
+
+[tool.ruff.lint]
+select = ["E", "F", "I", "UP", "B"]

alcedo_lit-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

alcedo_lit-0.1.0/src/alcedo_lit/__init__.py

@@ -0,0 +1,3 @@
+"""Alcedo: collect DOIs from a list of literature search queries, grouped by query."""
+
+__version__ = "0.1.0"

alcedo_lit-0.1.0/src/alcedo_lit/__main__.py

@@ -0,0 +1,6 @@
+import sys
+
+from .cli import main
+
+if __name__ == "__main__":
+    sys.exit(main())