From 3e47408963c157cef0f9e1c64f8bbf635bf1c1c9 Mon Sep 17 00:00:00 2001
From: Tim Holy <tim.holy@gmail.com>
Date: Fri, 10 May 2024 14:58:32 -0500
Subject: [PATCH 1/2] Formatting -> Format

Formatting.jl is now archived.

This also adds [compat] bounds on stdlibs.
---
 Project.toml           | 17 ++++++++++++++---
 src/PDB/PDB.jl         |  2 +-
 src/PDB/PDBParser.jl   |  6 +++---
 src/PDB/PDBResidues.jl |  2 +-
 4 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/Project.toml b/Project.toml
index 2ddb326e..8b75bc28 100644
--- a/Project.toml
+++ b/Project.toml
@@ -10,7 +10,7 @@ CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 FastaIO = "a0c94c4b-ebed-5953-b5fc-82fe598ac79f"
-Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
+Format = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LightXML = "9c8b4983-aa76-5018-a973-4c85ecc9e179"
@@ -36,22 +36,33 @@ ArgParse = "1"
 AutoHashEquals = "0.2, 1, 2"
 Clustering = "0.14, 0.15"
 CodecZlib = "0.6, 0.7"
+Dates = "1"
+DelimitedFiles = "1"
+Distributed = "1"
 Documenter = "0.21, 0.22, 0.23, 0.24, 0.25, 0.26, 0.27, 1"
 FastaIO = "1"
-Formatting = "0.4"
+Format = "1"
 HTTP = "0.9, 1"
 JSON = "0.21"
 LightXML = "0.8, 0.9"
+LinearAlgebra = "1"
+Logging = "1"
+Markdown = "1"
 NamedArrays = "=0.9.0, =0.9.1, =0.9.2, =0.9.3, =0.9.4, =0.9.5, =0.9.6"
+OrderedCollections = "1.1"
 PairwiseListMatrices = "0.11"
+Pkg = "1"
 ProgressMeter = "1"
+Random = "1"
 ROCAnalysis = "0.3"
 RecipesBase = "1"
 Requires = "1"
+Serialization = "1"
+Statistics = "1"
 StaticArrays = "0.12, 1.0"
 StatsBase = "0.32, 0.33, 0.34"
+Test = "1"
 TranscodingStreams = "0.9, 0.10"
-OrderedCollections = "1.1"
 julia = "1"
 
 [extras]
diff --git a/src/PDB/PDB.jl b/src/PDB/PDB.jl
index 7d9dfd06..ee5ce064 100644
--- a/src/PDB/PDB.jl
+++ b/src/PDB/PDB.jl
@@ -25,7 +25,7 @@ using LightXML
 using LinearAlgebra
 using Statistics            # mean
 using MIToS.Utils
-using Formatting
+using Format
 using JSON
 using HTTP
 using Logging
diff --git a/src/PDB/PDBParser.jl b/src/PDB/PDBParser.jl
index 9a486440..d8b8b862 100644
--- a/src/PDB/PDBParser.jl
+++ b/src/PDB/PDBParser.jl
@@ -64,8 +64,8 @@ function Base.parse(io::Union{IO,String}, ::Type{PDBFile};
             atom_chain = string(line[22])
             atom_name = String(strip(SubString(line, 13, 16), ' '))
             # PDB files generated by Foldseek have only CA atoms and no element identifier
-            # because they use only the first 66 columns of the file. We prefer using 
-            # `ncodeunits` over `length` since it's faster and `line` consists solely of 
+            # because they use only the first 66 columns of the file. We prefer using
+            # `ncodeunits` over `length` since it's faster and `line` consists solely of
             # ASCII characters.
             element = if 78 ≤ ncodeunits(line)
                 String(strip(SubString(line, 77, 78), ' '))
@@ -150,7 +150,7 @@ const _Format_PDB_ATOM = FormatExpr(
     #          1         2         3         4         5         6         7         8
     # 12345678901234567890123456789012345678901234567890123456789012345678901234567890
     # >    <>   < >  <|> < |>  <|   >      <>      <>      <>    <>    <      >  <><><
-    "{:<6}{:>5d} {:<4}{:>1}{:>3} {:>1}{:>4}{:>1}   {:>8.3f}{:>8.3f}{:>8.3f}{:>6.2f}{:>6.2f}      {:<4}{:>2}{:>2}\n"
+    "{:<6}{:>5d} {:<4}{:>1}{:>3} {:>1}{:>4}{:>1}   {:>8.3f}{:>8.3f}{:>8.3f}{:>6.2f}{:>6}      {:<4}{:>2}{:>2}\n"
     )
 
 # Models are numbered sequentially beginning with 1.
diff --git a/src/PDB/PDBResidues.jl b/src/PDB/PDBResidues.jl
index f843699e..705ed6d8 100644
--- a/src/PDB/PDBResidues.jl
+++ b/src/PDB/PDBResidues.jl
@@ -681,7 +681,7 @@ end
 #   (cross(points[2] - points[1], points[3] - points[1]), sum(points)./length(points))
 # end
 
-# Show PDB* objects (using Formatting)
+# Show PDB* objects (using Format)
 # ====================================
 
 const _Format_ResidueID = FormatExpr("{:>15} {:>15} {:>15} {:>15} {:>15} {:>15}\n")

From a69def0a72ba4c555ef47d2766fa6ef76b2d074d Mon Sep 17 00:00:00 2001
From: Tim Holy <tim.holy@gmail.com>
Date: Fri, 10 May 2024 15:26:26 -0500
Subject: [PATCH 2/2] Require Julia 1.6+

---
 .github/workflows/CI.yml | 1 -
 Project.toml             | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index ff01cde5..a25d854d 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -18,7 +18,6 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.0'
           - '1.6' # LTS
           - '1' # Latest Stable Release
         os:
diff --git a/Project.toml b/Project.toml
index 8b75bc28..b74faa25 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,6 +1,6 @@
 name = "MIToS"
 uuid = "51bafb47-8a16-5ded-8b04-24ef4eede0b5"
-version = "2.15.0"
+version = "2.16.0"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
@@ -63,7 +63,7 @@ StaticArrays = "0.12, 1.0"
 StatsBase = "0.32, 0.33, 0.34"
 Test = "1"
 TranscodingStreams = "0.9, 0.10"
-julia = "1"
+julia = "1.6"
 
 [extras]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"