pylsp black/isort formatting does not work

[carrascomj]

• nvim --version: v0.5.0-dev+1282-gfbe18d9ca
• nvim-lsp version(commit hash): 0a921bf
• What language server (If the problem is related to a specific language server): pylsp
• Can you reproduce this behavior on other language server clients (vscode, languageclient-neovim, coc.nvim, etc.): coc.nvim works fine (but I does not use pylsp).
• Can you reproduce this behavior on other language servers offered in the nvim-lspconfig repo? (pyls -> pyright): I had the same problems than with pyright but the efm was working right for that (although it had other problems).
• Is the problem isolated to a particular language server: I guess
• Operating system/version: Linux 5.12.1-arch1-1

How to reproduce the problem from neovim startup

Add this and load it in your config:

require"lspconfig".pylsp.setup {
    filetypes = {"python"},
    settings = {
        configurationSources = {"flake8"},
	formatCommand = {"black"}
    }
}

Then open a python file and, in command mode (:), run

:lua vim.lsp.buf.formatting()

Actual behaviour

No formatting occurs, sometimes this error is produced:

code_name = MethodNotFound, message = "method textDocument/formatting is not supported by any of the servers registered for the current buffer"

Apart from that, flake8 is not repecting my setup.cfg and returns the warnings from the default parameters.

Expected behaviour

With pyls-black installed, I would expect to run black on vim.lsp.buf.formatting(), but that's not the case. I guess that this is not implemented for pylsp and it may be hard since it is using its own plugins to handle formatting.

The same holds for pyls-isort.

Minimal init.vim or init.lua and code sample

Health check

Checkhealth result

health#lspconfig#check

Checking language server protocol configuration

• INFO: dockerls: configuration checked.
• INFO: pylsp: configuration checked.
• INFO: jsonls: configuration checked.
• INFO: rust_analyzer: configuration checked.
• INFO: sumneko_lua: configuration checked.

LSP log

Log file

[ START ] 2021-05-13T12:57:08+0200 ] LSP logging initiated [ INFO ] 2021-05-13T12:57:14+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:311 ] "Starting RPC client" { args = {}, cmd = "pylsp", extra = {}} [ DEBUG ] 2021-05-13T12:57:14+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:819 ] "LSP[pylsp]" "initialize_params" { capabilities = { callHierarchy = { dynamicRegistration = false, = <1>{ __tostring = } }, textDocument = { codeAction = { codeActionLiteralSupport = { codeActionKind = { valueSet = { "", "Empty", "QuickFix", "Refactor", "RefactorExtract", "RefactorInline", "RefactorRewrite", "Source", "SourceOrganizeImports", "quickfix", "refactor", "refactor.extract", "refactor.inline", "refactor.rewrite", "source", "source.organizeImports" }, = }, = }, dynamicRegistration = false, = }, completion = { completionItem = { commitCharactersSupport = false, deprecatedSupport = false, documentationFormat = { "markdown", "plaintext" }, preselectSupport = false, snippetSupport = false, = }, completionItemKind = { valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 }, = }, contextSupport = false, dynamicRegistration = false, = }, declaration = { linkSupport = true, = }, definition = { linkSupport = true, = }, documentHighlight = { dynamicRegistration = false, = }, documentSymbol = { dynamicRegistration = false, hierarchicalDocumentSymbolSupport = true, symbolKind = { valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 }, = }, = }, hover = { contentFormat = { "markdown", "plaintext" }, dynamicRegistration = false, = }, implementation = { linkSupport = true, = }, publishDiagnostics = { relatedInformation = true, tagSupport = { valueSet = { 1, 2 }, = }, = }, references = { dynamicRegistration = false, = }, rename = { dynamicRegistration = false, prepareSupport = true, = }, signatureHelp = { dynamicRegistration = false, signatureInformation = { documentationFormat = { "markdown", "plaintext" }, = }, = }, synchronization = { didSave = true, dynamicRegistration = false, willSave = false, willSaveWaitUntil = false, = }, typeDefinition = { linkSupport = true, = }, = }, window = { showDocument = { support = false, = }, showMessage = { messageActionItem = { additionalPropertiesSupport = false, = }, = }, workDoneProgress = true, = }, workspace = { applyEdit = true, configuration = true, symbol = { dynamicRegistration = false, hierarchicalWorkspaceSymbolSupport = true, symbolKind = { valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 }, = }, = }, workspaceEdit = { resourceOperations = { "rename", "create", "delete" }, = }, workspaceFolders = true, = } }, clientInfo = { name = "Neovim", version = "0.5.0" }, initializationOptions = vim.empty_dict(), processId = 1138576, rootPath = "/home/georg/GIT/dynamic-fba", rootUri = "file:///home/georg/GIT/dynamic-fba", trace = "off", workspaceFolders = { { name = "/home/georg/GIT/dynamic-fba", uri = "file:///home/georg/GIT/dynamic-fba" } }} [ DEBUG ] 2021-05-13T12:57:14+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { id = 1, jsonrpc = "2.0", method = "initialize", params = { capabilities = { callHierarchy = { dynamicRegistration = false, = <1>{ __tostring = } }, textDocument = { codeAction = { codeActionLiteralSupport = { codeActionKind = { valueSet = { "", "Empty", "QuickFix", "Refactor", "RefactorExtract", "RefactorInline", "RefactorRewrite", "Source", "SourceOrganizeImports", "quickfix", "refactor", "refactor.extract", "refactor.inline", "refactor.rewrite", "source", "source.organizeImports" }, = }, = }, dynamicRegistration = false, = }, completion = { completionItem = { commitCharactersSupport = false, deprecatedSupport = false, documentationFormat = { "markdown", "plaintext" }, preselectSupport = false, snippetSupport = false, = }, completionItemKind = { valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 }, = }, contextSupport = false, dynamicRegistration = false, = }, declaration = { linkSupport = true, = }, definition = { linkSupport = true, = }, documentHighlight = { dynamicRegistration = false, = }, documentSymbol = { dynamicRegistration = false, hierarchicalDocumentSymbolSupport = true, symbolKind = { valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 }, = }, = }, hover = { contentFormat = { "markdown", "plaintext" }, dynamicRegistration = false, = }, implementation = { linkSupport = true, = }, publishDiagnostics = { relatedInformation = true, tagSupport = { valueSet = { 1, 2 }, = }, = }, references = { dynamicRegistration = false, = }, rename = { dynamicRegistration = false, prepareSupport = true, = }, signatureHelp = { dynamicRegistration = false, signatureInformation = { documentationFormat = { "markdown", "plaintext" }, = }, = }, synchronization = { didSave = true, dynamicRegistration = false, willSave = false, willSaveWaitUntil = false, = }, typeDefinition = { linkSupport = true, = }, = }, window = { showDocument = { support = false, = }, showMessage = { messageActionItem = { additionalPropertiesSupport = false, = }, = }, workDoneProgress = true, = }, workspace = { applyEdit = true, configuration = true, symbol = { dynamicRegistration = false, hierarchicalWorkspaceSymbolSupport = true, symbolKind = { valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 }, = }, = }, workspaceEdit = { resourceOperations = { "rename", "create", "delete" }, = }, workspaceFolders = true, = } }, clientInfo = { name = "Neovim", version = "0.5.0" }, initializationOptions = vim.empty_dict(), processId = 1138576, rootPath = "/home/georg/GIT/dynamic-fba", rootUri = "file:///home/georg/GIT/dynamic-fba", trace = "off", workspaceFolders = { { name = "/home/georg/GIT/dynamic-fba", uri = "file:///home/georg/GIT/dynamic-fba" } } }} [ ERROR ] 2021-05-13T12:57:14+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:457 ] "rpc" "pylsp" "stderr" "2021-05-13 12:57:14,594 UTC - WARNING - pylsp.config.config - Failed to load pylsp entry point 'autopep8': No module named 'autopep8'\n" [ ERROR ] 2021-05-13T12:57:14+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:457 ] "rpc" "pylsp" "stderr" "2021-05-13 12:57:14,676 UTC - WARNING - pylsp.config.config - Failed to load pylsp entry point 'pylint': No module named 'pylint'\n" [ ERROR ] 2021-05-13T12:57:14+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:457 ] "rpc" "pylsp" "stderr" "2021-05-13 12:57:14,677 UTC - WARNING - pylsp.config.config - Failed to load pylsp entry point 'rope_completion': No module named 'rope'\n" [ ERROR ] 2021-05-13T12:57:14+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:457 ] "rpc" "pylsp" "stderr" "2021-05-13 12:57:14,679 UTC - WARNING - pylsp.config.config - Failed to load pylsp entry point 'rope_rename': No module named 'rope'\n" [ ERROR ] 2021-05-13T12:57:14+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:457 ] "rpc" "pylsp" "stderr" "2021-05-13 12:57:14,680 UTC - WARNING - pylsp.config.config - Failed to load pylsp entry point 'yapf': No module named 'yapf'\n" [ DEBUG ] 2021-05-13T12:57:15+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:491 ] "decoded" { id = 1, jsonrpc = "2.0", result = { capabilities = { codeActionProvider = true, codeLensProvider = { resolveProvider = false }, completionProvider = { resolveProvider = false, triggerCharacters = { "." } }, definitionProvider = true, documentFormattingProvider = true, documentHighlightProvider = true, documentRangeFormattingProvider = true, documentSymbolProvider = true, executeCommandProvider = { commands = {} }, experimental = vim.empty_dict(), foldingRangeProvider = true, hoverProvider = true, referencesProvider = true, renameProvider = true, signatureHelpProvider = { triggerCharacters = { "(", ",", "=" } }, textDocumentSync = { change = 2, openClose = true, save = { includeText = true } }, workspace = { workspaceFolders = { changeNotifications = true, supported = true } } } }} [ DEBUG ] 2021-05-13T12:57:15+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { jsonrpc = "2.0", method = "initialized", params = { [true] = 6 }} [ DEBUG ] 2021-05-13T12:57:15+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { jsonrpc = "2.0", method = "workspace/didChangeConfiguration", params = { settings = { configurationSources = { "flake8" }, formatCommand = { "isort" }, = { __tostring = } } }} [ DEBUG ] 2021-05-13T12:57:15+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:846 ] "LSP[pylsp]" "server_capabilities" { codeActionProvider = true, codeLensProvider = { resolveProvider = false }, completionProvider = { resolveProvider = false, triggerCharacters = { "." } }, definitionProvider = true, documentFormattingProvider = true, documentHighlightProvider = true, documentRangeFormattingProvider = true, documentSymbolProvider = true, executeCommandProvider = { commands = {} }, experimental = {}, foldingRangeProvider = true, hoverProvider = true, referencesProvider = true, renameProvider = true, signatureHelpProvider = { triggerCharacters = { "(", ",", "=" } }, textDocumentSync = { change = 2, openClose = true, save = { includeText = true } }, workspace = { workspaceFolders = { changeNotifications = true, supported = true } }} [ INFO ] 2021-05-13T12:57:15+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:847 ] "LSP[pylsp]" "initialized" { resolved_capabilities = { call_hierarchy = false, code_action = true, code_lens = true, code_lens_resolve = false, completion = true, declaration = false, document_formatting = true, document_highlight = true, document_range_formatting = true, document_symbol = true, execute_command = true, find_references = true, goto_definition = true, hover = true, implementation = false, rename = true, signature_help = true, signature_help_trigger_characters = { "(", ",", "=" }, text_document_did_change = 2, text_document_open_close = true, text_document_save = { includeText = true }, text_document_save_include_text = true, text_document_will_save = false, text_document_will_save_wait_until = false, type_definition = false, workspace_folder_properties = { changeNotifications = true, supported = true }, workspace_symbol = false }} [ DEBUG ] 2021-05-13T12:57:15+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { jsonrpc = "2.0", method = "textDocument/didOpen", params = { textDocument = { languageId = "python", text = '# Copyright (C) 2018, 2019 Columbia University Irving Medical Center,\n# New York, USA\n# Copyright (C) 2019 Novo Nordisk Foundation Center for Biosustainability,\n# Technical University of Denmark\n\n# This program is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n# the Free Software Foundation, either version 3 of the License, or\n# (at your option) any later version.\n\n# This program is distributed in the hope that it will be useful,\n# but WITHOUT ANY WARRANTY; without even the implied warranty of\n# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n# GNU General Public License for more details.\n\n# You should have received a copy of the GNU General Public License\n# along with this program. If not, see .\n\n"""Definition of `KineticVariable` class."""\n\nfrom numbers import Number\nfrom typing import Union\n\nfrom optlang import symbolics\n\nfrom .types import Expression\n\n\nclass KineticVariable(symbolics.Symbol):\n """Class for holding information for a kinetic variable in a `DfbaModel` object.\n\n Attributes\n ----------\n id: string\n The identifier to associate with this kinetic variable.\n\n rhs_expression: optlang.symbolics expression\n The symbolic expression for calculating derivative of this kinetic\n variable wrt time.\n\n initital_condition: int or float\n The initial value of this kinetic variable to be used at start of\n simulation.\n\n """\n\n def __init__(self, name: str, initial_condition: Number = 0.0, *args, **kwargs):\n """`symbolics.Symbol` with rhs expression to be added."""\n symbolics.Symbol.__init__(self, name, *args, **kwargs)\n self._id = name\n self.initial_condition = initial_condition\n self.rhs_expression = None\n\n @Property\n def id(self) -> str:\n """For convenience, synonym with .name from `symbolics.Symbol`."""\n return self._id\n\n @Property\n def rhs_expression(self) -> Union[Expression, None]:\n """Relate the rhs expression to some symbolic expression."""\n return self._rhs_expression\n\n @Property\n def initial_condition(self) -> Number:\n """Relate the ininital condition to some int or float value."""\n return self._initial_condition\n\n @rhs_expression.setter\n def rhs_expression(self, expression: Expression) -> None:\n self._rhs_expression = expression\n\n @initial_condition.setter\n def initial_condition(self, value: Expression) -> None:\n if not isinstance(value, (int, float)):\n raise Exception(\n f"Error: initial condition for kinetic variable {self.id} must"\n f"be int or float!"\n )\n self._initial_condition = value\n', uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py", version = 0 } }} [ DEBUG ] 2021-05-13T12:57:15+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/handlers.lua:442 ] "default_handler" "textDocument/publishDiagnostics" { client_id = 1, params = { diagnostics = {}, uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py" }} [ DEBUG ] 2021-05-13T12:57:16+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:491 ] "decoded" { jsonrpc = "2.0", method = "textDocument/publishDiagnostics", params = { diagnostics = { { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 29 }, start = { character = 79, line = 29 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 46 }, start = { character = 79, line = 46 } }, severity = 2, source = "pycodestyle" } }, uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py" }} [ DEBUG ] 2021-05-13T12:57:16+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:672 ] "notification" "textDocument/publishDiagnostics" { diagnostics = { { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 29 }, start = { character = 79, line = 29 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 46 }, start = { character = 79, line = 46 } }, severity = 2, source = "pycodestyle" } }, uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py"} [ DEBUG ] 2021-05-13T12:57:16+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/handlers.lua:442 ] "default_handler" "textDocument/publishDiagnostics" { client_id = 1, params = { diagnostics = { { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 29 }, start = { character = 79, line = 29 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 46 }, start = { character = 79, line = 46 } }, severity = 2, source = "pycodestyle" } }, uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py" }} [ DEBUG ] 2021-05-13T12:57:19+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:887 ] "LSP[pylsp]" "client.request" 1 "textDocument/formatting" { options = { insertSpaces = true, tabSize = 4 }, textDocument = { uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py" }} 1 [ DEBUG ] 2021-05-13T12:57:19+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { id = 2, jsonrpc = "2.0", method = "textDocument/formatting", params = { options = { insertSpaces = true, tabSize = 4 }, textDocument = { uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py" } }} [ DEBUG ] 2021-05-13T12:57:19+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:491 ] "decoded" { id = 2, jsonrpc = "2.0", result = vim.NIL} [ DEBUG ] 2021-05-13T12:57:19+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/handlers.lua:442 ] "default_handler" "textDocument/formatting" { bufnr = 1, client_id = 1} [ DEBUG ] 2021-05-13T12:57:26+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:991 ] "on_lines bufnr: 1, changedtick: 5, firstline: 25, lastline: 26, new_lastline: 26, old_byte_size: 30, old_utf32_size: 30, old_utf16_size: 30" { "from .types import Expression " } [ DEBUG ] 2021-05-13T12:57:26+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { jsonrpc = "2.0", method = "textDocument/didChange", params = { contentChanges = { { range = { end = { character = 29, line = 25 }, start = { character = 29, line = 25 } }, rangeLength = 0, text = " " } }, textDocument = { uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py", version = 5 } }} [ DEBUG ] 2021-05-13T12:57:26+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:991 ] "on_lines bufnr: 1, changedtick: 6, firstline: 25, lastline: 26, new_lastline: 26, old_byte_size: 31, old_utf32_size: 31, old_utf16_size: 31" { "from .types import Expression " } [ DEBUG ] 2021-05-13T12:57:26+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { jsonrpc = "2.0", method = "textDocument/didChange", params = { contentChanges = { { range = { end = { character = 30, line = 25 }, start = { character = 30, line = 25 } }, rangeLength = 0, text = " " } }, textDocument = { uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py", version = 6 } }} [ DEBUG ] 2021-05-13T12:57:26+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:991 ] "on_lines bufnr: 1, changedtick: 7, firstline: 25, lastline: 26, new_lastline: 26, old_byte_size: 32, old_utf32_size: 32, old_utf16_size: 32" { "from .types import Expression " } [ DEBUG ] 2021-05-13T12:57:26+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { jsonrpc = "2.0", method = "textDocument/didChange", params = { contentChanges = { { range = { end = { character = 31, line = 25 }, start = { character = 31, line = 25 } }, rangeLength = 0, text = " " } }, textDocument = { uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py", version = 7 } }} [ DEBUG ] 2021-05-13T12:57:26+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:991 ] "on_lines bufnr: 1, changedtick: 8, firstline: 25, lastline: 26, new_lastline: 26, old_byte_size: 33, old_utf32_size: 33, old_utf16_size: 33" { "from .types import Expression " } [ DEBUG ] 2021-05-13T12:57:26+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { jsonrpc = "2.0", method = "textDocument/didChange", params = { contentChanges = { { range = { end = { character = 32, line = 25 }, start = { character = 32, line = 25 } }, rangeLength = 0, text = " " } }, textDocument = { uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py", version = 8 } }} [ DEBUG ] 2021-05-13T12:57:27+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:491 ] "decoded" { jsonrpc = "2.0", method = "textDocument/publishDiagnostics", params = { diagnostics = { { code = "W291", message = "W291 trailing whitespace", range = { end = { character = 34, line = 25 }, start = { character = 29, line = 25 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 29 }, start = { character = 79, line = 29 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 46 }, start = { character = 79, line = 46 } }, severity = 2, source = "pycodestyle" } }, uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py" }} [ DEBUG ] 2021-05-13T12:57:27+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:672 ] "notification" "textDocument/publishDiagnostics" { diagnostics = { { code = "W291", message = "W291 trailing whitespace", range = { end = { character = 34, line = 25 }, start = { character = 29, line = 25 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 29 }, start = { character = 79, line = 29 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 46 }, start = { character = 79, line = 46 } }, severity = 2, source = "pycodestyle" } }, uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py"} [ DEBUG ] 2021-05-13T12:57:27+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/handlers.lua:442 ] "default_handler" "textDocument/publishDiagnostics" { client_id = 1, params = { diagnostics = { { code = "W291", message = "W291 trailing whitespace", range = { end = { character = 34, line = 25 }, start = { character = 29, line = 25 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 29 }, start = { character = 79, line = 29 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 46 }, start = { character = 79, line = 46 } }, severity = 2, source = "pycodestyle" } }, uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py" }} [ DEBUG ] 2021-05-13T12:57:27+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { jsonrpc = "2.0", method = "textDocument/didSave", params = { text = '# Copyright (C) 2018, 2019 Columbia University Irving Medical Center,\n# New York, USA\n# Copyright (C) 2019 Novo Nordisk Foundation Center for Biosustainability,\n# Technical University of Denmark\n\n# This program is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n# the Free Software Foundation, either version 3 of the License, or\n# (at your option) any later version.\n\n# This program is distributed in the hope that it will be useful,\n# but WITHOUT ANY WARRANTY; without even the implied warranty of\n# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n# GNU General Public License for more details.\n\n# You should have received a copy of the GNU General Public License\n# along with this program. If not, see .\n\n"""Definition of `KineticVariable` class."""\n\nfrom numbers import Number\nfrom typing import Union\n\nfrom optlang import symbolics\n\nfrom .types import Expression \n\n\nclass KineticVariable(symbolics.Symbol):\n """Class for holding information for a kinetic variable in a `DfbaModel` object.\n\n Attributes\n ----------\n id: string\n The identifier to associate with this kinetic variable.\n\n rhs_expression: optlang.symbolics expression\n The symbolic expression for calculating derivative of this kinetic\n variable wrt time.\n\n initital_condition: int or float\n The initial value of this kinetic variable to be used at start of\n simulation.\n\n """\n\n def __init__(self, name: str, initial_condition: Number = 0.0, *args, **kwargs):\n """`symbolics.Symbol` with rhs expression to be added."""\n symbolics.Symbol.__init__(self, name, *args, **kwargs)\n self._id = name\n self.initial_condition = initial_condition\n self.rhs_expression = None\n\n @Property\n def id(self) -> str:\n """For convenience, synonym with .name from `symbolics.Symbol`."""\n return self._id\n\n @Property\n def rhs_expression(self) -> Union[Expression, None]:\n """Relate the rhs expression to some symbolic expression."""\n return self._rhs_expression\n\n @Property\n def initial_condition(self) -> Number:\n """Relate the ininital condition to some int or float value."""\n return self._initial_condition\n\n @rhs_expression.setter\n def rhs_expression(self, expression: Expression) -> None:\n self._rhs_expression = expression\n\n @initial_condition.setter\n def initial_condition(self, value: Expression) -> None:\n if not isinstance(value, (int, float)):\n raise Exception(\n f"Error: initial condition for kinetic variable {self.id} must"\n f"be int or float!"\n )\n self._initial_condition = value\n', textDocument = { uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py" } }} [ DEBUG ] 2021-05-13T12:57:28+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:491 ] 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"file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py" }} [ DEBUG ] 2021-05-13T12:57:35+0200 ] /usr/share/nvim/runtime/lua/vim/lsp.lua:672 ] "notification" "textDocument/publishDiagnostics" { diagnostics = { { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 29 }, start = { character = 79, line = 29 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 46 }, start = { character = 79, line = 46 } }, severity = 2, source = "pycodestyle" } }, uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py"} [ DEBUG ] 2021-05-13T12:57:35+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/handlers.lua:442 ] "default_handler" "textDocument/publishDiagnostics" { client_id = 1, params = { diagnostics = { { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 29 }, start = { character = 79, line = 29 } }, severity = 2, source = "pycodestyle" }, { code = "E501", message = "E501 line too long (84 > 79 characters)", range = { end = { character = 85, line = 46 }, start = { character = 79, line = 46 } }, severity = 2, source = "pycodestyle" } }, uri = "file:///home/georg/GIT/dynamic-fba/src/dfba/variable.py" }} [ DEBUG ] 2021-05-13T12:57:37+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { jsonrpc = "2.0", method = "textDocument/didSave", params = { text = # This program is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n# the Free Software Foundation, either version 3 of the License, or\n# (at your option) any later version.\n\n# This program is distributed in the hope that it will be useful,\n# but WITHOUT ANY WARRANTY; without even the implied warranty of\n# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n# GNU General Public License for more details.\n\n# You should have received a copy of the GNU General Public License\n# along with this program. If not, see .\n\n"""Definition of `KineticVariable` class."""\n\nfrom numbers import Number\nfrom typing import Union\n\nfrom optlang import symbolics\n\nfrom .types import Expression\n\n\nclass KineticVariable(symbolics.Symbol):\n """Class for holding information for a kinetic variable in a `DfbaModel` object.\n\n Attributes\n ----------\n id: string\n The identifier to associate with this kinetic variable.\n\n rhs_expression: optlang.symbolics expression\n The symbolic expression for calculating derivative of this kinetic\n variable wrt time.\n\n initital_condition: int or float\n The initial value of this kinetic variable to be used at start of\n simulation.\n\n """\n\n def __init__(self, name: str, initial_condition: Number = 0.0, *args, **kwargs):\n """`symbolics.Symbol` with rhs expression to be added."""\n symbolics.Symbol.__init__(self, name, *args, **kwargs)\n self._id = name\n self.initial_condition = initial_condition\n self.rhs_expression = None\n\n @Property\n def id(self) 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= true, = }, workspace = { applyEdit = true, configuration = true, symbol = { dynamicRegistration = false, hierarchicalWorkspaceSymbolSupport = true, symbolKind = { valueSet = { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 }, = }, = }, workspaceEdit = { resourceOperations = { "rename", "create", "delete" }, = }, workspaceFolders = true, = } }, cmd = { "pylsp" }, filetypes = { "python" }, flags = {}, get_language_id = , handlers = <2>{}, init_options = vim.empty_dict(), log_level = 2, message_level = 2, name = "pylsp", on_attach = , on_exit = , on_init = , root_dir = "/home/georg/GIT/dynamic-fba", settings = { configurationSources = { "flake8" }, formatCommand = { "isort" }, = }, = }, handlers = , id = 1, initialized = true, is_stopped = , messages = { messages = {}, name = "pylsp", progress = {}, status = {} }, name = "pylsp", notify = , offset_encoding = "utf-16", request = , resolved_capabilities = { call_hierarchy = false, code_action = true, code_lens = true, code_lens_resolve = false, completion = true, declaration = false, document_formatting = true, document_highlight = true, document_range_formatting = true, document_symbol = true, execute_command = true, find_references = true, goto_definition = true, hover = true, implementation = false, rename = true, signature_help = true, signature_help_trigger_characters = <3>{ "(", ",", "=" }, text_document_did_change = 2, text_document_open_close = true, text_document_save = <4>{ includeText = true }, text_document_save_include_text = true, text_document_will_save = false, text_document_will_save_wait_until = false, type_definition = false, workspace_folder_properties = { changeNotifications = true, supported = true }, workspace_symbol = false }, rpc = { handle = , notify = , pid = 1139207, request = }, server_capabilities = { codeActionProvider = true, codeLensProvider = { resolveProvider = false }, completionProvider = { resolveProvider = false, triggerCharacters = { "." } }, definitionProvider = true, documentFormattingProvider = true, documentHighlightProvider = true, documentRangeFormattingProvider = true, documentSymbolProvider = true, executeCommandProvider = { commands = {} }, experimental = {}, foldingRangeProvider = true, hoverProvider = true, referencesProvider = true, renameProvider = true, signatureHelpProvider = { triggerCharacters = }, textDocumentSync = { change = 2, openClose = true, save = }, workspace = { workspaceFolders = { changeNotifications = true, supported = true } } }, stop = , supports_method = , workspaceFolders = { { name = "/home/georg/GIT/dynamic-fba", uri = "file:///home/georg/GIT/dynamic-fba" } }, workspace_did_change_configuration = } } [ DEBUG ] 2021-05-13T12:57:38+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { id = 5, jsonrpc = "2.0", method = "shutdown"} [ DEBUG ] 2021-05-13T12:57:38+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:491 ] "decoded" { id = 5, jsonrpc = "2.0", result = vim.NIL} [ DEBUG ] 2021-05-13T12:57:38+0200 ] /usr/share/nvim/runtime/lua/vim/lsp/rpc.lua:390 ] "rpc.send.payload" { jsonrpc = "2.0", method = "exit"}

[mjlbach]

Upstream issue: rupert/pyls-black#35

[carrascomj]

Oh, crap, I didn't see that (and it is very unfortunate). Thanks for the info!

[haplo]

@carrascomj Try python-lsp-black, which is a fork of pyls-black that is compatible with python-lsp-server. Just uninstall pyls-black and install the new one and it should work.

There is also a new release of pyls-isort that is compatible with python-lsp-server, so you should just need to upgrade it.

[carrascomj]

@haplo That's awesome, thank you very much! I tried and it works perfectly. It seems like it is the best LSP python server for neovim right now.

[mjlbach]

I personally find pyright significantly more performant FWIW

[carrascomj]

pyright was very good, but I could not get go-to-definition or formatting to work (I don't remember which one), but I might give it a try again.

[lithammer]

Pyright doesn't have formatting. You have to use something like diagnostic-languageserver or efm-langserver for that. Which I think is a more flexible solution anyway.

require("lspconfig").diagnosticls.setup {
  filetypes = {"python"},
  init_options = {
    formatters = {
      black = {
        command = "black",
        args = {"--quiet", "-"},
        rootPatterns = {"pyproject.toml"},
      },
      formatFiletypes = {
        python = {"black"}
      }
    }
  }
}

[nyngwang]

kindly link to the diagnostic-languageserver config by @lithammer for future readers reference.

[lithammer]

Note that I'm not very good at keeping that repo up-to-date. It might not even work with recent Neovim 0.6-0.7 changes.