From c5e59e5adfc1bd409a59a74920a592818b6d19eb Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 29 Jul 2024 11:18:18 +0200
Subject: [PATCH] removed outdated files

---
 DESCRIPTION                  |  4 +-
 conda/environment-build.yaml | 10 -----
 conda/environment.yaml       | 22 -----------
 conda/meta.yaml              | 77 ------------------------------------
 4 files changed, 2 insertions(+), 111 deletions(-)
 delete mode 100644 conda/environment-build.yaml
 delete mode 100644 conda/environment.yaml
 delete mode 100644 conda/meta.yaml

diff --git a/DESCRIPTION b/DESCRIPTION
index 5acef3f..22e1959 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: recetox.aplcms
 Title: Adaptive processing of LC-MS data
-Version: 0.12.0
-Date: 2023-07-10
+Version: 0.13.0
+Date: 2024-07-29
 Authors@R: c(
     person("Tianwei", "Yu", email = "tianwei.Yu@emory.edu", role = "aut"),
     person("Helge", family="Hecht", email = "helge.hecht@recetox.muni.cz", role = "cre"))
diff --git a/conda/environment-build.yaml b/conda/environment-build.yaml
deleted file mode 100644
index 79fe67b..0000000
--- a/conda/environment-build.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-name: recetox-aplcms-build
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - anaconda-client
-  - conda-build
-  - conda-verify
-  - r-base
diff --git a/conda/environment.yaml b/conda/environment.yaml
deleted file mode 100644
index 1b2776b..0000000
--- a/conda/environment.yaml
+++ /dev/null
@@ -1,22 +0,0 @@
-name: recetox-aplcms
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - r-base
-  - r-mass
-  - r-rgl
-  - bioconductor-mzR ==2.28.0
-  - r-splines2
-  - r-doparallel
-  - r-foreach
-  - r-snow
-  - r-rcpp
-  - r-arrow >=7.0.0,<10.0.0
-  - r-dplyr
-  - r-tidyr
-  - r-stringr
-  - r-tibble
-  - r-plyr
-
diff --git a/conda/meta.yaml b/conda/meta.yaml
deleted file mode 100644
index db4da35..0000000
--- a/conda/meta.yaml
+++ /dev/null
@@ -1,77 +0,0 @@
-{% set name = "recetox-aplcms" %}
-{% set version = "0.11.0" %}
-{% set github = "https://github.com/RECETOX" %}
-
-package:
-  name: "r-{{ name|lower }}"
-  version: "{{ version }}"
-
-source:
-  path: ..
-
-build:
-  number: 0
-  noarch: generic
-  rpaths:
-    - lib/R/lib/
-    - lib/
-  script_env:
-    - RGL_USE_NULL=TRUE # avoid warning at test-time
-  script: R CMD INSTALL --build . 
-  
-requirements:
-  host:
-    - r-base
-    - r-mass
-    - r-rgl
-    - bioconductor-mzR ==2.28.0
-    - r-splines2
-    - r-doparallel
-    - r-foreach
-    - r-snow
-    - r-rcpp
-    - r-arrow >=7.0.0,<10.0.0
-    - r-dplyr
-    - r-tidyr
-    - r-stringr
-    - r-tibble
-
-  run:
-    - r-base
-    - r-mass
-    - r-rgl
-    - bioconductor-mzR ==2.28.0
-    - r-splines2
-    - r-doparallel
-    - r-foreach
-    - r-snow
-    - r-rcpp
-    - r-arrow >=7.0.0,<10.0.0
-    - r-dplyr
-    - r-tidyr
-    - r-stringr
-    - r-tibble
-
-test:
-  commands:
-    - $R -e "library('recetox.aplcms')"
-
-about:
-  home: "{{ github }}"
-  license: GPL-2.0
-  license_file: LICENSE
-  summary: apLCMS is a software which generates a feature table from a batch of LC/MS spectra. A modified fork of the original apLCMS by Tianwei Yu.
-
-extra:
-  maintainers:
-    - hechth
-    - martenson
-    - maximskorik
-  identifiers:
-    - doi:10.1093/bioinformatics/btp291
-    - doi:10.1186/1471-2105-11-559
-    - doi:10.1021/pr301053d
-    - doi:10.1093/bioinformatics/btu430
-    - doi:10.1038/s41598-020-70850-0
-  container:
-    extended-base: True