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Read config #1

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Aug 9, 2023
Merged

Read config #1

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e87d39d
Add example via script
richfitz Aug 7, 2023
0b4fe82
Add basic config reader
richfitz Aug 7, 2023
761fa37
Update docs and tests
richfitz Aug 7, 2023
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12 changes: 12 additions & 0 deletions README.md
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pip install outpack
```

## Development

Useful hatch commands

```
hatch shell
hatch run test
hatch run cov
hatch run lint:style
hatch run lint:fmt
```

## License

`outpack` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.
1 change: 1 addition & 0 deletions example/.outpack/config.json
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{"schema_version":"0.1.0","core":{"path_archive":"archive","use_file_store":true,"require_complete_tree":false,"hash_algorithm":"sha256"},"logging":{"console":false,"threshold":"info"},"location":[{"name":"local","type":"local","args":{}}]}
2 changes: 2 additions & 0 deletions ...e/.outpack/files/sha256/2a/85eb5a027c8d2255e672d1592cc38c82cc0b08279b545a573ceccce9eb27cd
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"","a","b"
"1",1,"x"
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[{"topic":"name","detail":"data","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.1074},{"topic":"id","detail":"20230807-152345-1ad02157","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.10742},{"topic":"parameter","detail":["a: 2","b: y"],"caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.10745},{"topic":"start","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.10751},{"topic":"result","detail":"success","caller":"orderly2::orderly_run","log_level":"info","time":1691421825.10862},{"topic":"end","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.11338},{"topic":"elapsed","detail":"0.005954027 secs","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.11348}]
2 changes: 2 additions & 0 deletions ...e/.outpack/files/sha256/57/5b62d07fdf3fdf08c7272ae11a6322e5cbc907ee1dcb5d198bf9f900020619
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"","a","b"
"1",2,"x"
3 changes: 3 additions & 0 deletions ...e/.outpack/files/sha256/6e/e430041e1b83b72bac79a2e548a0450117dc763cc6ca71aca3bd2dbda6f520
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orderly2::orderly_parameters(a = NULL, b = NULL)
d <- data.frame(a = a, b = b)
write.csv(d, "data.csv")
2 changes: 2 additions & 0 deletions ...e/.outpack/files/sha256/70/95e31a5371a4fcf0e105e638d9a2d4229bb8d4253c426874511ec1ed64d685
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"","a","b"
"1",1,"y"
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[{"topic":"name","detail":"data","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.08179},{"topic":"id","detail":"20230807-152345-144cf26c","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.08181},{"topic":"parameter","detail":["a: 2","b: x"],"caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.08184},{"topic":"start","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.0819},{"topic":"result","detail":"success","caller":"orderly2::orderly_run","log_level":"info","time":1691421825.08294},{"topic":"end","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.08773},{"topic":"elapsed","detail":"0.005899668 secs","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.08782}]
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[{"topic":"name","detail":"data","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.05724},{"topic":"id","detail":"20230807-152345-0e0662d0","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.05725},{"topic":"parameter","detail":["a: 1","b: y"],"caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.05728},{"topic":"start","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.05734},{"topic":"result","detail":"success","caller":"orderly2::orderly_run","log_level":"info","time":1691421825.05834},{"topic":"end","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.06294},{"topic":"elapsed","detail":"0.005679131 secs","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.06303}]
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"","a","b"
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[{"topic":"name","detail":"data","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421824.93776},{"topic":"id","detail":"20230807-152344-ee606dce","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421824.93779},{"topic":"parameter","detail":["a: 1","b: x"],"caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421824.93785},{"topic":"start","detail":"2023-08-07 16:23:44","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421824.93795},{"topic":"result","detail":"success","caller":"orderly2::orderly_run","log_level":"info","time":1691421824.94152},{"topic":"end","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.03063},{"topic":"elapsed","detail":"0.09281063 secs","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.03146}]
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{"schema_version":"0.1.0","packet":"20230807-152344-ee606dce","time":1691421825.0517,"hash":"sha256:f46ff9faa7558a53e4144aaf2694912c15f8ca9fab3da050b320fa31cd9cbe15"}
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{"schema_version":"0.1.0","packet":"20230807-152345-0e0662d0","time":1691421825.0762,"hash":"sha256:81a8bd4c765760d148cfae6fdc4b2029727fbb0c14008d6518be7a20ef948f1e"}
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{"schema_version":"0.1.0","packet":"20230807-152345-144cf26c","time":1691421825.1015,"hash":"sha256:58cbb8f71f82684e9185891400a740901a504d1fff420b2c0ea5b6f44ce0c4d3"}
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{"schema_version":"0.1.0","packet":"20230807-152345-1ad02157","time":1691421825.1291,"hash":"sha256:35f6dc5060f774f26135d3a2f093118e6b31ee1f87aceb01a12d211a656d3085"}
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{"schema_version":"0.1.0","name":"data","id":"20230807-152344-ee606dce","time":{"start":1691421824.9377,"end":1691421825.0305},"parameters":{"a":1,"b":"x"},"files":[{"path":"data.csv","size":21,"hash":"sha256:2a85eb5a027c8d2255e672d1592cc38c82cc0b08279b545a573ceccce9eb27cd"},{"path":"log.json","size":896,"hash":"sha256:cfb4d4931dcbaef0e0edb2f77b8ed75a15e8b98eb4ce935909fe3c0f277440c9"},{"path":"orderly.R","size":104,"hash":"sha256:6ee430041e1b83b72bac79a2e548a0450117dc763cc6ca71aca3bd2dbda6f520"}],"depends":[],"git":{"sha":"407c7343fdfc1ff4d949b6719bd6977b96cf4fe6","branch":"config","url":["git@github.com:reside-ic/outpack-py.git"]},"custom":{"orderly":{"artefacts":[],"role":[{"path":"orderly.R","role":"orderly"},{"path":"log.json","role":"log"}],"description":{"display":null,"long":null,"custom":null},"shared":[],"session":{"platform":{"version":"R version 4.3.1 (2023-06-16)","os":"Ubuntu 20.04.6 LTS","system":"x86_64, linux-gnu"},"packages":[{"package":"orderly2","version":"1.99.2","attached":false},{"package":"utf8","version":"1.2.3","attached":false},{"package":"R6","version":"2.5.1","attached":false},{"package":"gert","version":"1.9000","attached":false},{"package":"magrittr","version":"2.0.3","attached":false},{"package":"glue","version":"1.6.2","attached":false},{"package":"tibble","version":"3.2.1","attached":false},{"package":"pkgconfig","version":"2.0.3","attached":false},{"package":"lifecycle","version":"1.0.3","attached":false},{"package":"cli","version":"3.6.1","attached":false},{"package":"askpass","version":"1.1","attached":false},{"package":"fansi","version":"1.0.4","attached":false},{"package":"openssl","version":"2.1.0","attached":false},{"package":"vctrs","version":"0.6.3","attached":false},{"package":"withr","version":"2.5.0","attached":false},{"package":"compiler","version":"4.3.1","attached":false},{"package":"sys","version":"3.4.2","attached":false},{"package":"credentials","version":"1.3.2","attached":false},{"package":"pillar","version":"1.9.0","attached":false},{"package":"yaml","version":"2.3.7","attached":false},{"package":"rlang","version":"1.1.1","attached":false},{"package":"jsonlite","version":"1.8.7","attached":false},{"package":"fs","version":"1.6.3","attached":false}]}}}}
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{"schema_version":"0.1.0","name":"data","id":"20230807-152345-0e0662d0","time":{"start":1691421825.0572,"end":1691421825.0629},"parameters":{"a":1,"b":"y"},"files":[{"path":"data.csv","size":21,"hash":"sha256:7095e31a5371a4fcf0e105e638d9a2d4229bb8d4253c426874511ec1ed64d685"},{"path":"log.json","size":897,"hash":"sha256:a3f318a59d7801e2ab1e403c65f4b225887a3ed4c5b7c97826d0d093ca5af309"},{"path":"orderly.R","size":104,"hash":"sha256:6ee430041e1b83b72bac79a2e548a0450117dc763cc6ca71aca3bd2dbda6f520"}],"depends":[],"git":{"sha":"407c7343fdfc1ff4d949b6719bd6977b96cf4fe6","branch":"config","url":["git@github.com:reside-ic/outpack-py.git"]},"custom":{"orderly":{"artefacts":[],"role":[{"path":"orderly.R","role":"orderly"},{"path":"log.json","role":"log"}],"description":{"display":null,"long":null,"custom":null},"shared":[],"session":{"platform":{"version":"R version 4.3.1 (2023-06-16)","os":"Ubuntu 20.04.6 LTS","system":"x86_64, linux-gnu"},"packages":[{"package":"orderly2","version":"1.99.2","attached":false},{"package":"utf8","version":"1.2.3","attached":false},{"package":"R6","version":"2.5.1","attached":false},{"package":"gert","version":"1.9000","attached":false},{"package":"magrittr","version":"2.0.3","attached":false},{"package":"glue","version":"1.6.2","attached":false},{"package":"tibble","version":"3.2.1","attached":false},{"package":"pkgconfig","version":"2.0.3","attached":false},{"package":"lifecycle","version":"1.0.3","attached":false},{"package":"cli","version":"3.6.1","attached":false},{"package":"askpass","version":"1.1","attached":false},{"package":"fansi","version":"1.0.4","attached":false},{"package":"openssl","version":"2.1.0","attached":false},{"package":"vctrs","version":"0.6.3","attached":false},{"package":"withr","version":"2.5.0","attached":false},{"package":"compiler","version":"4.3.1","attached":false},{"package":"sys","version":"3.4.2","attached":false},{"package":"credentials","version":"1.3.2","attached":false},{"package":"pillar","version":"1.9.0","attached":false},{"package":"yaml","version":"2.3.7","attached":false},{"package":"rlang","version":"1.1.1","attached":false},{"package":"jsonlite","version":"1.8.7","attached":false},{"package":"fs","version":"1.6.3","attached":false}]}}}}
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{"schema_version":"0.1.0","name":"data","id":"20230807-152345-144cf26c","time":{"start":1691421825.0818,"end":1691421825.0877},"parameters":{"a":2,"b":"x"},"files":[{"path":"data.csv","size":21,"hash":"sha256:575b62d07fdf3fdf08c7272ae11a6322e5cbc907ee1dcb5d198bf9f900020619"},{"path":"log.json","size":896,"hash":"sha256:78f16fdefa2e7a921fadec936a9b076d853d1f0ae8135396944af4e650ff4968"},{"path":"orderly.R","size":104,"hash":"sha256:6ee430041e1b83b72bac79a2e548a0450117dc763cc6ca71aca3bd2dbda6f520"}],"depends":[],"git":{"sha":"407c7343fdfc1ff4d949b6719bd6977b96cf4fe6","branch":"config","url":["git@github.com:reside-ic/outpack-py.git"]},"custom":{"orderly":{"artefacts":[],"role":[{"path":"orderly.R","role":"orderly"},{"path":"log.json","role":"log"}],"description":{"display":null,"long":null,"custom":null},"shared":[],"session":{"platform":{"version":"R version 4.3.1 (2023-06-16)","os":"Ubuntu 20.04.6 LTS","system":"x86_64, linux-gnu"},"packages":[{"package":"orderly2","version":"1.99.2","attached":false},{"package":"utf8","version":"1.2.3","attached":false},{"package":"R6","version":"2.5.1","attached":false},{"package":"gert","version":"1.9000","attached":false},{"package":"magrittr","version":"2.0.3","attached":false},{"package":"glue","version":"1.6.2","attached":false},{"package":"tibble","version":"3.2.1","attached":false},{"package":"pkgconfig","version":"2.0.3","attached":false},{"package":"lifecycle","version":"1.0.3","attached":false},{"package":"cli","version":"3.6.1","attached":false},{"package":"askpass","version":"1.1","attached":false},{"package":"fansi","version":"1.0.4","attached":false},{"package":"openssl","version":"2.1.0","attached":false},{"package":"vctrs","version":"0.6.3","attached":false},{"package":"withr","version":"2.5.0","attached":false},{"package":"compiler","version":"4.3.1","attached":false},{"package":"sys","version":"3.4.2","attached":false},{"package":"credentials","version":"1.3.2","attached":false},{"package":"pillar","version":"1.9.0","attached":false},{"package":"yaml","version":"2.3.7","attached":false},{"package":"rlang","version":"1.1.1","attached":false},{"package":"jsonlite","version":"1.8.7","attached":false},{"package":"fs","version":"1.6.3","attached":false}]}}}}
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{"schema_version":"0.1.0","name":"data","id":"20230807-152345-1ad02157","time":{"start":1691421825.1074,"end":1691421825.1133},"parameters":{"a":2,"b":"y"},"files":[{"path":"data.csv","size":21,"hash":"sha256:a666a5bc8fa211cfcd1561b051a1f32f4d7730f9fd1295d4ca893009ffba6e98"},{"path":"log.json","size":896,"hash":"sha256:2d0edf86db715c06ed0392f2f4adff16b292eb8a8d170f135d6c8c10ad033571"},{"path":"orderly.R","size":104,"hash":"sha256:6ee430041e1b83b72bac79a2e548a0450117dc763cc6ca71aca3bd2dbda6f520"}],"depends":[],"git":{"sha":"407c7343fdfc1ff4d949b6719bd6977b96cf4fe6","branch":"config","url":["git@github.com:reside-ic/outpack-py.git"]},"custom":{"orderly":{"artefacts":[],"role":[{"path":"orderly.R","role":"orderly"},{"path":"log.json","role":"log"}],"description":{"display":null,"long":null,"custom":null},"shared":[],"session":{"platform":{"version":"R version 4.3.1 (2023-06-16)","os":"Ubuntu 20.04.6 LTS","system":"x86_64, linux-gnu"},"packages":[{"package":"orderly2","version":"1.99.2","attached":false},{"package":"utf8","version":"1.2.3","attached":false},{"package":"R6","version":"2.5.1","attached":false},{"package":"gert","version":"1.9000","attached":false},{"package":"magrittr","version":"2.0.3","attached":false},{"package":"glue","version":"1.6.2","attached":false},{"package":"tibble","version":"3.2.1","attached":false},{"package":"pkgconfig","version":"2.0.3","attached":false},{"package":"lifecycle","version":"1.0.3","attached":false},{"package":"cli","version":"3.6.1","attached":false},{"package":"askpass","version":"1.1","attached":false},{"package":"fansi","version":"1.0.4","attached":false},{"package":"openssl","version":"2.1.0","attached":false},{"package":"vctrs","version":"0.6.3","attached":false},{"package":"withr","version":"2.5.0","attached":false},{"package":"compiler","version":"4.3.1","attached":false},{"package":"sys","version":"3.4.2","attached":false},{"package":"credentials","version":"1.3.2","attached":false},{"package":"pillar","version":"1.9.0","attached":false},{"package":"yaml","version":"2.3.7","attached":false},{"package":"rlang","version":"1.1.1","attached":false},{"package":"jsonlite","version":"1.8.7","attached":false},{"package":"fs","version":"1.6.3","attached":false}]}}}}
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[{"topic":"name","detail":"data","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421824.93776},{"topic":"id","detail":"20230807-152344-ee606dce","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421824.93779},{"topic":"parameter","detail":["a: 1","b: x"],"caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421824.93785},{"topic":"start","detail":"2023-08-07 16:23:44","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421824.93795},{"topic":"result","detail":"success","caller":"orderly2::orderly_run","log_level":"info","time":1691421824.94152},{"topic":"end","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.03063},{"topic":"elapsed","detail":"0.09281063 secs","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.03146}]
3 changes: 3 additions & 0 deletions example/archive/data/20230807-152344-ee606dce/orderly.R
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orderly2::orderly_parameters(a = NULL, b = NULL)
d <- data.frame(a = a, b = b)
write.csv(d, "data.csv")
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"","a","b"
"1",1,"y"
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[{"topic":"name","detail":"data","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.05724},{"topic":"id","detail":"20230807-152345-0e0662d0","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.05725},{"topic":"parameter","detail":["a: 1","b: y"],"caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.05728},{"topic":"start","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.05734},{"topic":"result","detail":"success","caller":"orderly2::orderly_run","log_level":"info","time":1691421825.05834},{"topic":"end","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.06294},{"topic":"elapsed","detail":"0.005679131 secs","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.06303}]
3 changes: 3 additions & 0 deletions example/archive/data/20230807-152345-0e0662d0/orderly.R
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orderly2::orderly_parameters(a = NULL, b = NULL)
d <- data.frame(a = a, b = b)
write.csv(d, "data.csv")
2 changes: 2 additions & 0 deletions example/archive/data/20230807-152345-144cf26c/data.csv
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"","a","b"
"1",2,"x"
1 change: 1 addition & 0 deletions example/archive/data/20230807-152345-144cf26c/log.json
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[{"topic":"name","detail":"data","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.08179},{"topic":"id","detail":"20230807-152345-144cf26c","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.08181},{"topic":"parameter","detail":["a: 2","b: x"],"caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.08184},{"topic":"start","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.0819},{"topic":"result","detail":"success","caller":"orderly2::orderly_run","log_level":"info","time":1691421825.08294},{"topic":"end","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.08773},{"topic":"elapsed","detail":"0.005899668 secs","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.08782}]
3 changes: 3 additions & 0 deletions example/archive/data/20230807-152345-144cf26c/orderly.R
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orderly2::orderly_parameters(a = NULL, b = NULL)
d <- data.frame(a = a, b = b)
write.csv(d, "data.csv")
2 changes: 2 additions & 0 deletions example/archive/data/20230807-152345-1ad02157/data.csv
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"","a","b"
"1",2,"y"
1 change: 1 addition & 0 deletions example/archive/data/20230807-152345-1ad02157/log.json
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[{"topic":"name","detail":"data","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.1074},{"topic":"id","detail":"20230807-152345-1ad02157","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.10742},{"topic":"parameter","detail":["a: 2","b: y"],"caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.10745},{"topic":"start","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_start","log_level":"info","time":1691421825.10751},{"topic":"result","detail":"success","caller":"orderly2::orderly_run","log_level":"info","time":1691421825.10862},{"topic":"end","detail":"2023-08-07 16:23:45","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.11338},{"topic":"elapsed","detail":"0.005954027 secs","caller":"orderly2::outpack_packet_end","log_level":"info","time":1691421825.11348}]
3 changes: 3 additions & 0 deletions example/archive/data/20230807-152345-1ad02157/orderly.R
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orderly2::orderly_parameters(a = NULL, b = NULL)
d <- data.frame(a = a, b = b)
write.csv(d, "data.csv")
1 change: 1 addition & 0 deletions example/orderly_config.yml
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minimum_orderly_version: "1.99.0"
3 changes: 3 additions & 0 deletions example/src/data/orderly.R
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orderly2::orderly_parameters(a = NULL, b = NULL)
d <- data.frame(a = a, b = b)
write.csv(d, "data.csv")
4 changes: 3 additions & 1 deletion pyproject.toml
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Expand Up @@ -24,7 +24,9 @@ classifiers = [
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python :: Implementation :: PyPy",
]
dependencies = []
dependencies = [
"dataclasses-json"
]

[project.urls]
Documentation = "https://github.com/mrc-ide/outpack#readme"
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23 changes: 23 additions & 0 deletions scripts/generate_examples
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#!/usr/bin/env Rscript

# Until we implement enough of outpack-py, we won't be able to
# bootstrap our own example code to read, so this generates a little
# example set.
root <- gert::git_find()
path <- file.path(root, "example")
unlink(path, recursive = TRUE)
orderly2::orderly_init(path, logging_console = FALSE, use_file_store = TRUE)

path_src <- file.path(path, "src", "data")
fs::dir_create(path_src)
writeLines(
c("orderly2::orderly_parameters(a = NULL, b = NULL)",
"d <- data.frame(a = a, b = b)",
'write.csv(d, "data.csv")'),
file.path(path_src, "orderly.R"))

for (a in 1:2) {
for (b in c("x", "y")) {
orderly2::orderly_run("data", list(a = a, b = b), root = path)
}
}
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