Merge commit '24fe235ec6bffc125db90997b5db5f559e9bbb6b'

Author: the-mayer

.Rbuildignore

@@ -5,7 +5,10 @@
 ^docs$
 ^pkgdown$
 ^.lintr$
-.vscode/
+.vscode$
 ^\.github$
 terraform/
 DEVELOPER.md
+^README\.Rmd$
+^CODE_OF_CONDUCT\.md$
+

.gitignore

@@ -2,4 +2,6 @@ inst/doc
 **/.quarto/
 docs
 .vscode/
-terraform/
+terraform/
+/.quarto/
+**/*.quarto_ipynb

CODE_OF_CONDUCT.md

@@ -0,0 +1,139 @@
+# Code of Conduct
+
+We abide the [CU code of conduct](https://www.cu.edu/ope/aps/2027) as part of our association with the University of Colorado Anshutz Medical Campus.
+
+Additionally, we follow the Contributor Covenant Code of Conduct, as found below.
+
+## Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socioeconomic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+- Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+- The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to community leaders responsible for enforcement.
+Please open a [new security advisory notice](https://github.com/CU-DBMI/.github/security/advisories/new) (using defaults or “n/a” where unable to fill in the form) to privately notify us of any incidents of this nature.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][mozilla coc].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][faq]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[faq]: https://www.contributor-covenant.org/faq
+[homepage]: https://www.contributor-covenant.org
+[mozilla coc]: https://github.com/mozilla/diversity
+[translations]: https://www.contributor-covenant.org/translations
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: programets
 Title: Collect and analyze academic impact metrics from various sources
-Version: 0.2.0
+Version: 0.3.0
 Authors@R: 
     c(person("Sean", "Davis", , "[email protected]", role = c("aut", "cre"), comment=c(ORCID = "0000-0002-8991-6458")),
     person("David", "Mayer", , "[email protected]", role = c("aut")))
@@ -14,18 +14,23 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
+Depends:
+    R (>= 4.1.0)
 Imports:
     googleAnalyticsR,
     dplyr,
     rlang,
     utils,
-    httr2,
     purrr,
+    httr2,
     jsonlite,
     stringr,
-    tibble
+    tibble,
+    glue,
+    ghql
 Suggests:
     gargle,
+    gitcreds,
     knitr,
     quarto,
     lubridate,

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2025
-COPYRIGHT HOLDER: programets authors
+COPYRIGHT HOLDER: programets authors

NAMESPACE

@@ -1,27 +1,52 @@
 # Generated by roxygen2: do not edit by hand
 
+export(epmc_search)
 export(ga_dataframe)
 export(ga_meta_simple)
 export(ga_query_explorer)
-export(get_publications_for_core_projects)
+export(get_core_project_info)
+export(get_github_by_topic)
+export(get_github_by_topic_graphql)
 export(icite)
 import(dplyr)
 import(httr2)
 import(jsonlite)
 importFrom(dplyr,arrange)
+importFrom(dplyr,as_tibble)
 importFrom(dplyr,bind_rows)
+importFrom(dplyr,filter)
+importFrom(dplyr,full_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,relocate)
 importFrom(dplyr,tibble)
+importFrom(ghql,GraphqlClient)
+importFrom(glue,glue)
+importFrom(glue,glue_collapse)
+importFrom(httr2,req_auth_bearer_token)
 importFrom(httr2,req_body_json)
+importFrom(httr2,req_error)
 importFrom(httr2,req_headers)
 importFrom(httr2,req_method)
 importFrom(httr2,req_perform)
+importFrom(httr2,req_perform_parallel)
+importFrom(httr2,req_retry)
+importFrom(httr2,req_url_query)
 importFrom(httr2,request)
 importFrom(httr2,resp_body_json)
+importFrom(httr2,resp_status)
+importFrom(jsonlite,fromJSON)
+importFrom(purrr,discard)
+importFrom(purrr,map2_dbl)
+importFrom(purrr,map_chr)
+importFrom(purrr,map_dbl)
 importFrom(purrr,map_dfr)
+importFrom(purrr,pmap)
+importFrom(rlang,"%||%")
 importFrom(rlang,.data)
 importFrom(rlang,abort)
 importFrom(rlang,format_error_bullets)
 importFrom(rlang,inform)
+importFrom(stats,setNames)
 importFrom(stringr,regex)
 importFrom(stringr,str_detect)
+importFrom(tibble,tibble)