Merge pull request #25 from starius/fix-luacheck-warnings

Fix luacheck warnings

.travis.yml

@@ -23,7 +23,7 @@ install:
   - luarocks make --local CFLAGS="-O0 -fPIC -ftest-coverage -fprofile-arcs" LIBFLAG="-shared --coverage"
 
 script:
-  - if [[ "$LUA" != *"luajit"* ]]; then .travis/lua-globals.sh `find src -name '*.lua'`; fi
+  - luacheck `find src -name '*.lua'`
   - tar -cf /tmp/lua-src.tar.gz src/npge/*.lua src/npge/*/*.lua
   - rm src/npge/*.lua src/npge/*/*.lua
   - export LD_PRELOAD=/lib/x86_64-linux-gnu/libpthread.so.0

.travis/setup_rocks.sh

@@ -6,3 +6,4 @@ luarocks install luaposix --local
 luarocks install lua-rote --local
 luarocks install alnbox --local
 luarocks install tree --local
+luarocks install luacheck --local

src/npge/algo/Blast.lua

@@ -37,7 +37,7 @@ function Blast.checkNoCollisions(bs1, bs2)
     end
 end
 
-function Blast.blastnCmd(bank_fname, query_fname, options)
+function Blast.blastnCmd(bank_fname, query_fname)
     local config = require 'npge.config'
     local nullName = require 'npge.util.nullName'
     local args = {

src/npge/algo/BlastHits.lua

@@ -20,7 +20,7 @@ local function readBlast(file, query, bank, same, line_handler)
         return query_name and bank_name
             and query_row and bank_row
     end
-    local function goodFragments(query_f, bank_f)
+    local function goodFragments(_, _)
         return true
     end
     if same then
@@ -96,8 +96,8 @@ local function readBlast(file, query, bank, same, line_handler)
             query_row = {}
             bank_row = {}
         elseif goodHit() then
-            local function parseAlignment(line)
-                local parts = split(line)
+            local function parseAlignment(line1)
+                local parts = split(line1)
                 assert(#parts == 4 or #parts == 3)
                 if #parts == 4 then
                     local _, start, row, stop = unpack(parts)

src/npge/algo/CheckPangenome.lua

@@ -64,7 +64,7 @@ return function(blockset)
     -- block must be in right orientation
     -- Quality of s,h,r-blocks is part of this step
     for block, name in blockset:iterBlocks() do
-        local t, size, length, n = npge.block.parseName(name)
+        local t, size, length, _ = npge.block.parseName(name)
         if size ~= block:size() then
             fail("Block %s has size %d", name, block:size())
         end
@@ -104,9 +104,9 @@ return function(blockset)
                 warning([[ All of these good parts were
                     eliminated by better or equal blocks]])
             else
-                local names = blockNames(better_parts)
+                local better_names = blockNames(better_parts)
                 fail(" The following %d parts can be added: %s",
-                    #better_parts, names)
+                    #better_parts, better_names)
             end
         end
     end
@@ -125,7 +125,7 @@ return function(blockset)
     local joined = npge.algo.Join(blockset)
     warning("Joining neighbour blocks produces %d blocks",
         joined:size())
-    for i, block in ipairs(joined:blocks()) do
+    for _, block in ipairs(joined:blocks()) do
         local block_name = npge.block.giveName(block, #genomes)
         inspectBlock('Joined ' .. block_name, block)
     end

src/npge/algo/JoinMinor.lua

@@ -41,7 +41,7 @@ local function joinMinor(block, bs, joined, joinable)
             local Block = require 'npge.model.Block'
             local minor_block = Block(fragments)
             table.insert(joined, minor_block)
-            for neighbour, f_ori in pairs(neighbours[ori]) do
+            for neighbour, _ in pairs(neighbours[ori]) do
                 joinable[neighbour]  = nil
             end
         end

src/npge/algo/Merge.lua

@@ -19,7 +19,7 @@ return function(blocksets)
         end
     end
     local seqs = {}
-    for name, seq in pairs(name2seq) do
+    for _, seq in pairs(name2seq) do
         table.insert(seqs, seq)
     end
     local concatArrays = require 'npge.util.concatArrays'

src/npge/algo/Multiply.lua

@@ -28,7 +28,7 @@ local function Multiply(bs1, bs2)
                 end
             end
         end
-        for block2, oo in pairs(block2_to_fragments) do
+        for _, oo in pairs(block2_to_fragments) do
             -- TODO preserve alignment
             table.insert(blocks, model.Block(oo))
         end

src/npge/algo/NonCovered.lua

@@ -19,7 +19,7 @@ return function(blockset)
         local fragments = {}
         local last_pos = seq:length() - 1
         local prev
-        for fragment, part in blockset:iterFragments(seq) do
+        for _, part in blockset:iterFragments(seq) do
             local last = prev and max(prev) or -1
             local first = min(part)
             if first - last > 1 then

src/npge/algo/Overlapping.lua

@@ -7,13 +7,13 @@ return function(blockset, block)
     for f1 in block:iterFragments() do
         local fragments = blockset:overlappingFragments(f1)
         for _, f2 in ipairs(fragments) do
-            local block = blockset:blockByFragment(f2)
-            blocks_set[block] = true
+            local block1 = blockset:blockByFragment(f2)
+            blocks_set[block1] = true
         end
     end
     local blocks = {}
-    for block, _ in pairs(blocks_set) do
-        table.insert(blocks, block)
+    for block1, _ in pairs(blocks_set) do
+        table.insert(blocks, block1)
     end
     return blocks
 end

src/npge/algo/PrimaryHits.lua

@@ -10,7 +10,7 @@ return function(blockset)
     local Genomes = require 'npge.algo.Genomes'
     local has_genomes, _, genome2seqs = pcall(Genomes, blockset)
     if has_genomes then
-        for genome, seqs in pairs(genome2seqs) do
+        for _, seqs in pairs(genome2seqs) do
             table.insert(level2bss[1], BlockSet(seqs, {}))
         end
     else
@@ -35,7 +35,7 @@ return function(blockset)
     end
 
     local niterations = #(level2bss[1]) - 1
-    for i = 1, niterations do
+    for _ = 1, niterations do
         local a, level_a = assert(popBs())
         local b, level_b = assert(popBs())
         local Cover = require 'npge.algo.Cover'

src/npge/algo/UnwindBlocks.lua

@@ -5,7 +5,7 @@
 local function mergeSequences(prefix2blockset)
     local blocksets = {}
     local BlockSet = require 'npge.model.BlockSet'
-    for prefix, blockset in pairs(prefix2blockset) do
+    for _, blockset in pairs(prefix2blockset) do
         local seqs = blockset:sequences()
         table.insert(blocksets, BlockSet(seqs, {}))
     end

src/npge/alignment/alignRows.lua

@@ -9,7 +9,7 @@ local function compress(rows)
     -- returns new rows, decompression_info
     local new_rows = {}
     local decompression_info = {}
-    for i, row in ipairs(rows) do
+    for _, row in ipairs(rows) do
         if #row >= 1 then
             table.insert(new_rows, row)
             table.insert(decompression_info, #new_rows)
@@ -74,7 +74,7 @@ end
 
 local function emptyRows(n)
     local rows = {}
-    for i = 1, n do
+    for _ = 1, n do
         table.insert(rows, '')
     end
     return rows

src/npge/alignment/complementRows.lua

@@ -5,7 +5,7 @@
 return function(rows)
     local new_rows = {}
     local complement = require 'npge.alignment.complement'
-    for i, row in ipairs(rows) do
+    for _, row in ipairs(rows) do
         table.insert(new_rows, complement(row))
     end
     return new_rows

src/npge/block/slice.lua

@@ -23,7 +23,6 @@ return function(block, min, max, row)
     assert(#row >= (max - min + 1))
     local for_block = {}
     for fragment in block:iterFragments() do
-        local seq = fragment:sequence()
         local frag_min = block:block2right(fragment, min)
         local frag_max = block:block2left(fragment, max)
         if frag_min ~= -1 and frag_max ~= -1 and

src/npge/config.lua

@@ -43,7 +43,7 @@ local about = {}
 for section_name, section in pairs(config) do
     about[section_name] = {}
     local names = {}
-    for name, value_and_desc in pairs(section) do
+    for name, _ in pairs(section) do
         table.insert(names, name)
     end
     for _, name in ipairs(names) do
@@ -80,7 +80,7 @@ end
 local function loadConfig(_, conf)
     local sandbox = require 'npge.util.sandbox'
     local env = {}
-    for section_name, section in pairs(config) do
+    for section_name, _ in pairs(config) do
         env[section_name] = {}
     end
     env.Decimal = function() end -- C++ NPGe compatibility

src/npge/io/LoadFromLua.lua

@@ -37,7 +37,7 @@ return function(code, enable_fromRef)
         next=next, pairs=pairs, pcall=pcall,
         tonumber=tonumber, tostring=tostring,
         type=type,
-        unpack = unpack or table.unpack,
+        unpack = _G.unpack or table.unpack,
         string = {
             byte=string.byte, char=string.char,
             format=string.format, len=string.len,

src/npge/io/ReadFromBs.lua

@@ -38,9 +38,9 @@ local function isParted(start, stop, ori)
     return diff * ori < 0
 end
 
-local function getParts(seqname, start, stop, ori, text)
+local function getParts(seqname, start, stop, ori, text0)
     local toAtgcn = require 'npge.alignment.toAtgcn'
-    local text = toAtgcn(text)
+    local text = toAtgcn(text0)
     local length = #text
     local length1, length2
     if ori == 1 then
@@ -113,7 +113,6 @@ local function readWithoutReference(generator)
     local seqname2parts = {}
     local ev = require 'npge.util.extractValue'
     local Sequence = require 'npge.model.Sequence'
-    local parseId = require 'npge.fragment.parseId'
     for name, description, text in generator do
         local blockname = ev(description, "block")
         if blockname then
@@ -145,7 +144,7 @@ local function readWithoutReference(generator)
         collectgarbage() -- large text
     end
     local sequences = {}
-    for name, seq in pairs(seqname2seq) do
+    for _, seq in pairs(seqname2seq) do
         table.insert(sequences, seq)
     end
     return sequences, blockname2fragments
@@ -183,7 +182,6 @@ return function(lines, blockset_with_sequences)
     local bs1 = BlockSet(sequences, {})
     local blocks = {}
     for blockname, fr_descs in pairs(blockname2fragments) do
-        local Block = require 'npge.model.Block'
         blocks[blockname] = makeBlock(bs1, fr_descs)
     end
     return BlockSet(sequences, blocks)

src/npge/io/ShortForm.lua

@@ -279,7 +279,7 @@ function ShortForm.decode(iterator, seq_bs)
     local loader, env = ShortForm.loaderAndEnv()
     local sandbox = require 'npge.util.sandbox'
     for line in iterator do
-        local f, err = assert(sandbox(env, line))
+        local f, _ = assert(sandbox(env, line))
         f()
     end
     return ShortForm.loader2blockset(loader, seq_bs)

src/npge/util/loadstring.lua

@@ -2,4 +2,4 @@
 -- Copyright (C) 2014-2016 Boris Nagaev
 -- See the LICENSE file for terms of use.
 
-return loadstring or load
+return _G.loadstring or _G.load

src/npge/util/mapItems.lua

@@ -5,7 +5,7 @@
 -- map items to ngroups groups of almost equal size
 return function(ngroups, items)
     local groups = {}
-    for i = 1, ngroups do
+    for _ = 1, ngroups do
         table.insert(groups, {})
     end
     math.randomseed(os.time())

src/npge/util/sandbox.lua

@@ -19,13 +19,13 @@ return function(env, code)
         _VERSION == 'Lua 5.3',
         'Implemented in Lua 5.1, 5.2 and 5.3 only')
     if _VERSION == 'Lua 5.2' or _VERSION == 'Lua 5.3' then
-        return load(code, 'sandbox', 't', env)
+        return _G.load(code, 'sandbox', 't', env)
     elseif _VERSION == 'Lua 5.1' then
-        local f, message = loadstring(code, 'sandbox')
+        local f, message = _G.loadstring(code, 'sandbox')
         if not f then
             return nil, message
         end
-        setfenv(f, env)
+        _G.setfenv(f, env)
         return f
     end
 end

src/npge/util/threads.lua

@@ -63,7 +63,6 @@ return function(generator, collector)
         local result = loadstring(code)()
         return collector({result})
     end
-    local config = require 'npge.config'
     local conf = config:save()
     local threads = spawnWorkers(generator, workers, conf)
     return collectResults(collector, threads)

src/npge/util/unpack.lua

@@ -2,4 +2,4 @@
 -- Copyright (C) 2014-2016 Boris Nagaev
 -- See the LICENSE file for terms of use.
 
-return unpack or table.unpack
+return _G.unpack or table.unpack