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Joao P Dubas
8dffb86d01
chore(deps): update deps of deps
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2024-07-08 21:36:37 +00:00
Joao P Dubas
866730238e
feat(deps): upgrade req from 0.5.0 to 0.5.2 2024-07-08 21:28:35 +00:00
Joao P Dubas
eeb6964348
merge: updates from upstream 
Conflicts:
    mix.lock
 2024-07-08 21:25:21 +00:00
Joao P Dubas
3f83808335 feat: upgrade elixir and erlang runtimes, and deps (#83)
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Upgrade runtimes:

* [erlang from 26.2.5 to 27.0][0]
* [elixir from 1.16.3 to 1.17.1][1]

Upgrade dependencies:

* `castore` [from 1.0.6 to 1.0.8](https://diff.hex.pm/diff/castore/1.0.6..1.0.8)
* `cowboy` [from 2.10.0 to 2.12.0](https://diff.hex.pm/diff/cowboy/2.10.0..2.12.0)
* `cowlib` [from 2.12.1 to 2.13.0](https://diff.hex.pm/diff/cowlib/2.12.1..2.13.0)
* `credo` [from 1.7.6 to 1.7.7](https://diff.hex.pm/diff/credo/1.7.6..1.7.7)
* `db_connection` [from 2.6.0 to 2.7.0](https://diff.hex.pm/diff/db_connection/2.6.0..2.7.0)
* `ecto_sql` [from 3.11.2 to 3.11.3](https://diff.hex.pm/diff/ecto_sql/3.11.2..3.11.3)
* `erlex` [from 0.2.6 to 0.2.7](https://diff.hex.pm/diff/erlex/0.2.6..0.2.7)
* `hpax` [from 0.1.2 to 1.0.0](https://diff.hex.pm/diff/hpax/0.1.2..1.0.0)
* `jason` [from 1.4.1 to 1.4.3](https://diff.hex.pm/diff/jason/1.4.1..1.4.3)
* `mime` [from 2.0.5 to 2.0.6](https://diff.hex.pm/diff/mime/2.0.5..2.0.6)
* `mint` [from 1.5.2 to 1.6.2](https://diff.hex.pm/diff/mint/1.5.2..1.6.2)
* `nimble_options` [from 1.1.0 to 1.1.1](https://diff.hex.pm/diff/nimble_options/1.1.0..1.1.1)
* `nimble_pool` [from 1.0.0 to 1.1.0](https://diff.hex.pm/diff/nimble_pool/1.0.0..1.1.0)
* `phoenix` [from 1.7.12 to 1.7.14](https://diff.hex.pm/diff/phoenix/1.7.12..1.7.14)
* `phoenix_ecto` [from 4.6.1 to 4.6.2](https://diff.hex.pm/diff/phoenix_ecto/4.6.1..4.6.2)
* `phoenix_live_dashboard` [from 0.8.3 to 0.8.4](https://diff.hex.pm/diff/phoenix_live_dashboard/0.8.3..0.8.4)
* `phoenix_live_view` [from 0.20.14 to 0.20.17](https://diff.hex.pm/diff/phoenix_live_view/0.20.14..0.20.17)
* `phoenix_view` [from 2.0.3 to 2.0.4](https://diff.hex.pm/diff/phoenix_view/2.0.3..2.0.4)
* `plug` [from 1.15.3 to 1.16.1](https://diff.hex.pm/diff/plug/1.15.3..1.16.1)
* `plug_crypto` [from 2.0.0 to 2.1.0](https://diff.hex.pm/diff/plug_crypto/2.0.0..2.1.0)
* `telemetry_metrics_prometheus_core` [from 1.2.0 to 1.2.1](https://diff.hex.pm/diff/telemetry_metrics_prometheus_core/1.2.0..1.2.1)
* `websock_adapter` [from 0.5.5 to 0.5.6](https://diff.hex.pm/diff/websock_adapter/0.5.5..0.5.6)
* `yaml_elixir` [from 2.9.0 to 2.11.0](https://diff.hex.pm/diff/yaml_elixir/2.9.0..2.11.0)

To make `graphql` work with the newer `erlang` and `elixir`, the `absinthe` is installed directly from github:

* [`absinthe`](358e273a26)
* [`absinthe_plug`](3a984cc341)

Finally, the `ci` routine was simplified, so test + lint is executed in parallel, and more core is reused.

[0]: https://www.erlang.org/news/170
[1]: https://github.com/elixir-lang/elixir/releases/tag/v1.17.1

Reviewed-on: #83
Co-authored-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
Co-committed-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
 2024-07-08 21:04:26 +00:00
Joao P Dubas
0d7a4cc9c3
chore(growth): move nil logic to scorer behaviour
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Handle `nil` measurement in `Growth.Score.Scorer`.
 2024-06-11 14:53:19 +00:00
Joao P Dubas
7fab746ea8
feat: add ex_doc to generate documentation
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2024-06-11 12:18:18 +00:00
Joao P Dubas
c81e4fda67
chore(growth): add log in loader
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2024-06-11 12:02:14 +00:00
Joao P Dubas
bc9c2124f1
chore(growth): add example for Growth.new/4 2024-06-11 12:01:50 +00:00
Joao P Dubas
c14a26a184
fix(growth): measure for subscapular skinfold 2024-06-11 12:01:25 +00:00
Joao P Dubas
79aec9f7e5
feat(growth): calculate z-score/centile for all indicators
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2024-06-11 11:42:57 +00:00
Joao P Dubas
2545a796c3
chore(growth): return nil when measure isn't set 2024-06-11 11:42:17 +00:00
Joao P Dubas
88b8e811a8
chore(growth): apply scorer behaviour in indicators 2024-06-11 11:41:31 +00:00
Joao P Dubas
fa022b9592
feat(growth): calculate z-score/centile for all indicators 
The `Growth.Score.Scorer` behaviour implements the methods needed to
calculate z-score and centile for any indicator.
 2024-06-11 11:38:18 +00:00
Joao P Dubas
0ac434c61d
fix(growth): ignore enum result explicitly
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2024-06-10 19:24:41 +00:00
Joao P Dubas
06b35cbceb
wip(growth): implement results for bmi
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This implementation should be made generic for all other scores.
 2024-06-10 19:09:35 +00:00
Joao P Dubas
28f0546bcb
chore(growth): add default value for results 2024-06-10 18:35:12 +00:00
Joao P Dubas
c175c3edfd
fix(growth): typespec and doc for centile calc 2024-06-10 18:34:24 +00:00
Joao P Dubas
4234b2e917
chore(growth): load is independent from task
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Details 
Ensure that `Growth.Indicators.Load.all/0` can be run independently from
the task.

So, the `ets` table is create based on the filename processed.
 2024-06-10 13:01:44 +00:00
Joao P Dubas
04fff60541
wip(growth): add score module
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Details 
This module is responsible for calculate the z score/centile for each
measurement.
 2024-06-10 12:15:16 +00:00
Joao P Dubas
b415b38184
feat(growth): load data on application start 
To make this possible, the following changes were made:

* Use `Task` to start the load process
* Create `ets` table before start the async task
  * This is needed to keep the tables alive after the task process exits
* Adjust the application to start the `Growth.Indicators.Load` task
 2024-06-10 12:11:18 +00:00
Joao P Dubas
412250d7ef
feat(growth): add struct to represent measurement
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2024-06-09 20:00:49 +00:00
Joao P Dubas
d3c1aa9b6b
chore(growth): improve age documentation and typing 2024-06-09 19:59:33 +00:00
Joao P Dubas
025ab1537d
chore(growth): name ets tables with score modules 2024-06-09 19:58:34 +00:00
Joao P Dubas
52c1d0c028
feat(growth): load csv indicators into ets tables
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2024-06-07 13:28:13 +00:00
Joao P Dubas
902a22c947
chore(growth): fetch extended data for indicators
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Also, improve module doc.
 2024-06-06 22:49:52 +00:00
Joao P Dubas
a8466f0c1d
chore(growth): add documentation and examples
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2024-06-06 20:39:10 +00:00
Joao P Dubas
bb79aa2f3a fix(growth): alias z-score and use if
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2024-06-06 11:34:02 +00:00
Joao P Dubas
500d0e89bb
wip(growth): calculate key metrics for growth
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Details 
1. calculate age in days, weeks, and months
2. calculate body mass index for metric and english unities
3. calculate z-score for a given measurement and box-cox parameters (l,
   m, s)
4. calculate centile score for a given measurement and box-cox
   parameters
 2024-06-06 01:36:11 +00:00
Joao P Dubas
8be9fa38bb
wip(growth): add fix note on convert/3 method
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2024-06-04 23:56:27 +00:00
Joao P Dubas
9c8e1d20ee
wip(growth): improve data parsing 
1. Fetch common data for all indicators
2. Remove headers during merge

Also, re-generate files.
 2024-06-04 23:55:03 +00:00
Joao P Dubas
2fedb4ecf0
wip(growth): change from with to case
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2024-06-04 14:36:20 +00:00
Joao P Dubas
58f14c0346
wip(growth): fetch|extract|save indicators from WHO 
Initial implementation to fetch growth indicators from WHO.

For now, the system merges the measurements for each gender and age
group in a single `csv` file.

The final solution should do this, saving a `dets` file.
 2024-06-04 13:57:32 +00:00
Joao P Dubas
ece17e3cf9 feat: upgrade elixir runtimes and dependencies (#78)
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Details 
Upgrade [elixir][0] runtime from [1.16.2 to 1.16.3][1].

Also, [upgrade application dependencies][2]:

* `ecto_sql` from 3.11.1 to 3.11.2
* `phoenix_ecto` from 4.6.0 to 4.6.1
* `postgrex` from 0.17.5 to 0.18.0

Reviewed-on: #78

[0]: https://github.com/elixir-lang/elixir/releases/tag/v1.16.3
[1]: https://github.com/elixir-lang/elixir/compare/v1.16.2...v1.16.3
[2]: https://diff.hex.pm/diffs?diffs[]=ecto_sql:3.11.1:3.11.2&diffs[]=phoenix_ecto:4.6.0:4.6.1&diffs[]=postgrex:0.17.5:0.18.0
Co-authored-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
Co-committed-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
 2024-05-28 14:27:49 +00:00
Joao P Dubas
e616d01e63 chore(ci): upgrade database and erlang runtime on pipelines (#74)
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The following upgrades were made:

* Bump [`postgres` from 16.0 to 16.3][postgres-release].
* Bump [`erlang`][erlang-release] from [26.2.3 to 26.2.5][erlang-diffs].

Also, use the same `elixir` image/tag on both pipelines.

[postgres-release]: https://www.postgresql.org/docs/release/16.3/
[erlang-release]: https://www.erlang.org/patches/otp-26.2.5
[erlang-diffs]: https://github.com/erlang/otp/compare/OTP-26.2.3...OTP-26.2.5

Reviewed-on: #74
Co-authored-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
Co-committed-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
 2024-05-16 19:15:12 +00:00
Joao P Dubas
9aeaaabc35 chore(deps): upgrade erlang runtime and application dependencies (#73)
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Bump [application dependencies][app-diffs]:

* [`credo` from 1.7.5 to 1.7.6][credo-diffs]
* [`phoenix_ecto` from 4.5.1. to 4.6.0][phoenix_ecto-diffs]

Bump [`erlang`][erlang-release] from [26.2.3 to 26.2.5][erlang-diffs].

[app-diffs]: https://diff.hex.pm/diffs?diffs[]=credo:1.7.5:1.7.6&diffs[]=phoenix_ecto:4.5.1:4.6.0
[credo-diffs]: https://diff.hex.pm/diff/credo/1.7.5..1.7.6
[phoenix_ecto-diffs]: https://diff.hex.pm/diff/phoenix_ecto/4.5.1..4.6.0
[erlang-release]: https://www.erlang.org/patches/otp-26.2.5
[erlang-diffs]: https://github.com/erlang/otp/compare/OTP-26.2.3...OTP-26.2.5

Reviewed-on: #73
Co-authored-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
Co-committed-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
 2024-05-16 18:46:25 +00:00
renovate-bot
de9fa663c9 chore(deps): update postgres docker tag to v16.3 (#71)
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This PR contains the following updates:

| Package | Update | Change |
|---|---|---|
| postgres | minor | `16.2-alpine` -> `16.3-alpine` |

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Reviewed-on: #71
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 2024-05-10 13:53:46 +00:00
Joao P Dubas
037f4d7504 feat(deps): bump application dependencies (#70)
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Details 
[Bump dependencies][0]:

1. junit_formatter from 3.3.1 to 3.4.0
2. phoenix from 1.7.11 to 1.7.12
3. plug_cowboy from 2.7.0 to 2.7.1
4. telemetry_poller from 1.0.0 to 1.1.0

[0]: https://diff.hex.pm/diffs?diffs%5B%5D=junit_formatter:3.3.1:3.4.0&diffs%5B%5D=phoenix:1.7.11:1.7.12&diffs%5B%5D=plug_cowboy:2.7.0:2.7.1&diffs%5B%5D=telemetry_poller:1.0.0:1.1.0

Co-authored-by: renovate-bot <renovate-bot@dubas.dev>
Reviewed-on: #70
Co-authored-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
Co-committed-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
 2024-04-15 14:18:49 +00:00
Joao P Dubas
9bd41ba3b8 chore(deps): bump erlang runtime and deps (#67)
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Update runtime:

* Bump [`erlang` from 26.2.2 to 26.2.3][0]

Update [dependencies][1]:

* credo from 1.7.4 to 1.7.5
* mix_audit from 2.1.2 to 2.1.3
* phoenix_ecto from 4.4.3 to 4.5.1
* postgrex from 0.17.4 to 0.17.5

[0]: https://www.erlang.org/patches/otp-26.2.3
[1]: https://diff.hex.pm/diffs?diffs[]=credo:1.7.4:1.7.5&diffs[]=mix_audit:2.1.2:2.1.3&diffs[]=phoenix_ecto:4.4.5:4.5.1&diffs[]=postgrex:0.17.4:0.17.5

Reviewed-on: #67
Co-authored-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
Co-committed-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
 2024-03-19 16:23:27 +00:00
renovate-bot
dbce23e51a chore(deps): update hexpm/elixir docker tag to v1.16.2 (#65)
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This PR contains the following updates:

| Package | Type | Update | Change |
|---|---|---|---|
| hexpm/elixir | final | patch | `1.16.1-erlang-26.2.2-debian-bookworm-20240130-slim` -> `1.16.2-erlang-26.2.2-debian-bookworm-20240130-slim` |

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Reviewed-on: #65
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 2024-03-19 12:48:38 +00:00
renovate-bot
2fca7bc67d chore(deps): update dependency elixir to v1.16.2 (#64)
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This PR contains the following updates:

| Package | Update | Change |
|---|---|---|
| [elixir](https://elixir-lang.org/) ([source](https://github.com/elixir-lang/elixir)) | patch | `1.16.1` -> `1.16.2` |

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Reviewed-on: #64
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 2024-03-19 11:52:41 +00:00
renovate-bot
0f4cedf078 chore(deps): update postgres docker tag to v16.2 (#62)
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This PR contains the following updates:

| Package | Update | Change |
|---|---|---|
| postgres | minor | `16.1-alpine` -> `16.2-alpine` |

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This PR has been generated by [Renovate Bot](https://github.com/renovatebot/renovate).
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Reviewed-on: #62
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 2024-02-25 11:04:15 +00:00
Joao P Dubas
24d75a2fd8 feat(ci): trigger on branch main (#61)
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Reviewed-on: #61
Co-authored-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
Co-committed-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
 2024-02-11 14:09:51 +00:00
João Paulo Dubas
1b21556d2c Upgrade runtime and deps (#60) 
Upgrade project runtimes and dependencies to the latest versions.

1. Runtimes:
    1. `elixir` to 1.16.1
    1. `erlang` to 26.2.2
1. [Dependencies][0]:
    1. `absinte` from 1.7.5 to 1.7.6
    1. `credo` from 1.7.1 to 1.7.4
    1. `dialyxir` from 1.4.2 to 1.4.3
    1. `ecto_sql` from 3.10.3 to 3.11.1
    1. `gettext` from 0.23.1 to 0.24.0
    1. `mix_audit` from 2.1.1 to 2.1.2
    1. `pg_ranges` from 1.1.0 to 1.1.1
    1. `phoenix` from 1.7.10 to 1.7.11
    1. `plug_cowboy` from 2.6.1 to 2.7.0
    1. `postgrex` from 0.17.3 to 0.17.4
    1. `telemetry_metrics` from 0.6.1 to 0.6.2

[0]: https://diff.hex.pm/diffs?diffs[]=absinte:1.7.5:1.7.6&diffs[]=credo:1.7.1:1.7.4&diffs[]=dialyxir:1.4.2:1.4.3&diffs[]=ecto_sql:3.10.3:3.11.1&diffs[]=gettext:0.23.1:0.24.0&diffs[]=mix_audit:2.1.1:2.1.2&diffs[]=pg_ranges:1.1.0:1.1.1&diffs[]=phoenix:1.7.10:1.7.11&diffs[]=plug_cowboy:2.6.1:2.7.0&diffs[]=postgrex:0.17.3:0.17.4&diffs[]=telemetry_metrics:0.6.1:0.6.2

Reviewed-on: #60
 2024-02-11 13:53:11 +00:00
renovate-bot
4d09f20e69 chore(deps): update elixir docker tag (#56) 
This PR contains the following updates:

| Package | Type | Update | Change |
|---|---|---|---|
| elixir | final | minor | `1.15.7-slim` -> `1.16.0-slim` |
| [elixir](https://elixir-lang.org/) ([source](https://github.com/elixir-lang/elixir)) |  | minor | `1.15.7` -> `1.16.1` |

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 2024-01-31 11:42:10 +00:00
renovate-bot
42ae54b17e chore(deps): update dependency sobelow to ~> 0.13 (#51) 
This PR contains the following updates:

| Package | Update | Change |
|---|---|---|
| [sobelow](https://hex.pm/packages/sobelow) | minor | `~> 0.12` -> `~> 0.13` |

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Reviewed-on: #51
Co-authored-by: renovate-bot <renovate-bot@dubas.dev>
Co-committed-by: renovate-bot <renovate-bot@dubas.dev>
 2023-11-25 16:58:29 +00:00
renovate-bot
93e1719d0d chore(deps): update postgres docker tag to v16.1 (#52) 
This PR contains the following updates:

| Package | Update | Change |
|---|---|---|
| postgres | minor | `16.0-alpine` -> `16.1-alpine` |

---

This PR has been generated by [Renovate Bot](https://github.com/renovatebot/renovate).
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Reviewed-on: #52
Co-authored-by: renovate-bot <renovate-bot@dubas.dev>
Co-committed-by: renovate-bot <renovate-bot@dubas.dev>
 2023-11-24 15:13:48 +00:00
João Paulo Dubas
7420139650 feat(ci): additional code/deps/security checks (#37) 
To improve `CI` quality the following checks were added:

* compile warnings
* deprecated dependencies
* insecure dependencies
* unused dependencies
* code vulnerabilities

Also, to improve `CI` execution time, dependencies checks and lining were separated from the test pipeline.

Last, but not least, to make local development easier a `Dockerfile` was created to contain any system dependencies, and targets to handle database creation and migration were added.

Reviewed-on: #37
 2023-11-11 20:35:45 +00:00
Joao P Dubas
62219ecc9f chore(deps): upgrade locked deps (#50) 
After running `mix do deps.unlock --all, deps.clean --all, clean, deps.get` the following dependencies were updated:

```
credo ................... 1.7.0 ... 1.7.1
db_connection ........... 2.5.0 ... 2.6.0
dialyxir ................ 1.4.0 ... 1.4.2
ecto_sql ................ 3.10.1 .. 3.10.2
gettext ................. 0.23.0 .. 0.23.1
phoenix ................. 1.7.9 ... 1.7.10
phoenix_ecto ............ 4.4.2 ... 4.4.3
phoenix_live_dashboard .. 0.8.0 ... 0.8.3
phoenix_live_view ....... 0.19.5 .. 0.20.1
phoenix_view ............ 2.0.2 ... 2.0.3
postgrex ................ 0.17.1 .. 0.17.3
websock_adapter ......... 0.5.4 ... 0.5.5
```

For a detailed diff view check [diff.hex.pm][0].

[0]: https://diff.hex.pm/diffs?diffs[]=credo:1.7.0:1.7.1&diffs[]=db_connection:2.5.0:2.6.0&diffs[]=dialyxir:1.4.0:1.4.2&diffs[]=ecto_sql:3.10.1:3.10.2&diffs[]=gettext:0.23.0:0.23.1&diffs[]=phoenix:1.7.9:1.7.10&diffs[]=phoenix_ecto:4.4.2:4.4.3&diffs[]=phoenix_live_dashboard:0.8.0:0.8.3&diffs[]=phoenix_live_view:0.19.5:0.20.1&diffs[]=phoenix_view:2.0.2:2.0.3&diffs[]=postgrex:0.17.1:0.17.3&diffs[]=websock_adapter:0.5.4:0.5.5

Reviewed-on: #50
Co-authored-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
Co-committed-by: Joao P Dubas <joao.dubas+gitea@gmail.com>
 2023-11-11 19:00:26 +00:00
renovate-bot
88de0beeac chore(deps): update elixir docker tag to v1.15.7 (#49) 
This PR contains the following updates:

| Package | Type | Update | Change |
|---|---|---|---|
| elixir | docker | patch | `1.15.6-slim` -> `1.15.7-slim` |
| elixir |  | patch | `1.15.6-slim` -> `1.15.7-slim` |
| [elixir](https://elixir-lang.org/) ([source](https://github.com/elixir-lang/elixir)) |  | patch | `1.15.6` -> `1.15.7` |

---

This PR has been generated by [Renovate Bot](https://github.com/renovatebot/renovate).
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Reviewed-on: #49
Co-authored-by: renovate-bot <renovate-bot@dubas.dev>
Co-committed-by: renovate-bot <renovate-bot@dubas.dev>
 2023-11-09 21:47:25 +00:00
renovate-bot
d7c99b099d chore(deps): update dependency prom_ex to ~> 1.9.0 (#48) 
This PR contains the following updates:

| Package | Update | Change |
|---|---|---|
| [prom_ex](https://hex.pm/packages/prom_ex) | minor | `~> 1.8.0` -> `~> 1.9.0` |

---

This PR has been generated by [Renovate Bot](https://github.com/renovatebot/renovate).
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Reviewed-on: #48
Co-authored-by: renovate-bot <renovate-bot@dubas.dev>
Co-committed-by: renovate-bot <renovate-bot@dubas.dev>
 2023-10-12 21:47:51 +00:00